After Sept. 11, America’s genius for innovation seemed to hold the promise of protection from future terrorist attacks. As Congress debated how much of the nation’s commerce should be scanned, sniffed or X-rayed, private contractors rushed to the new Homeland Security Department with all manner of chemical sensors, retina scanners, digital databases and borderland monitors.

But it was clear even then that the country’s safety would rely more on skilled people than on scanners: intelligence officers, infantrymen, food inspectors, customs agents, passenger screeners, chemical experts, forensic linguists, border patrollers, and all sorts of other watchers, listeners and analysts.

Six years later, the government is still struggling to complete this human element of the homeland-protection mission — filling thousands of jobs, up and down the chain of command. When the right people are found for the more challenging positions, their training is time-consuming and expensive. Background checks and security clearances can take up to two years, during which time some qualified candidates simply abandon the notion of government service. The good workers who endure the process sometimes don’t stay long enough to justify the government’s investment in them, because they’re lured away by more creative and lucrative work in the private sector.

The Army, burdened by combat in Iraq and Afghanistan, has not met its recruiting goals for the past two months, despite lowering its standards for those with medical problems or criminal histories. Recruiters say it will be difficult to reach the goals again for a long time. The CIA and other intelligence agencies have plenty of applicants, but they are having trouble finding crucial specialists, such as linguists fluent in Arabic.

At the Homeland Security Department, where low morale has become endemic, airport security screeners are leaving at the rate of 14 percent to 17 percent a year, roughly four times the government average. Strong leadership might help, but almost a quarter of the department’s top executive jobs are currently vacant.

Since 2001, the federal government has added an estimated 137,000 new positions at the departments of Homeland Security and State, the FBI, the military and the intelligence community. That does not count millions of contractors hired for military and other national security-related missions, nor the thousands of new security personnel scattered among departments from Energy to Treasury.

National security, in fact, has driven the increase in the size of the federal government. The Partnership for Public Service, a nonprofit organization that promotes public-sector employment, estimates that the government will need 63,000 new workers in security fields in the next two years.

In the face of this demand, federal agencies are having a difficult time recruiting, training and retaining enough qualified employees to protect against terrorist and other threats. The task has become simply overwhelming.

A number of experts and several top agency officials agree that finding and keeping the best people is the most important key to keeping the nation safe. The cost of failure is quite literally the difference between life and death.

If the United States had enough translators on the job in the summer of 2001 it might not have missed the fabled “zero hour” clue — when spy agencies on Sept. 10 intercepted a communication by an Arabic speaker declaring that “tomorrow is zero hour,” but did not translate the declaration in time. If officials with backgrounds in governmental disaster response had been leading the Federal Emergency Management Agency in 2005, perhaps hundreds more would have survived Hurricane Katrina.

“The government is only as good as its people,” said Max Stier, the president and chief executive officer of Partnership for Public Service. “If we are unable to attract and retain top people in government, we will not be able to address the serious challenges that face our nation.”

The chief human capital officer for the Office of the Director of National Intelligence, Ronald P. Sanders, says that at the root of the intelligence overhaul law, enacted three years ago in response to recommendations of the independent Sept. 11 commission, was a simple theme: human resources.

“I think the transformation of the intelligence community is largely about people,” Sanders said. “There’s clearly a technological component to it as well. But even technology — the research, design and deployment — hinges on having very talented people.” Some of the Bush administration’s responses to the personnel strain have only exacerbated the problems.

A new personnel system at Homeland Security, which gives managers more leeway in promotions and discipline, has contributed to low morale, which, in turn, contributes to rapid turnover.

By relying heavily upon contractors to handle work since Sept. 11, the intelligence community inadvertently helped bolster the private-sector intelligence market to the point that some veteran intelligence professionals have left, lured by the rich salaries, only to return to work at the spy agencies as contractors, at a higher expense.

This is not to say that departments such as Defense and Homeland Security haven’t been able to work some prodigies during the past five years. They have. Homeland’s much maligned Transportation Security Administration was able to field tens of thousands of airport security workers within months of the system’s creation, albeit with the help of a private hiring contractor that cost more than $700 million.

And the challenges that security agencies face in recruiting and retention are common throughout the government, particularly as the baby boom generation begins to retire and the private economy expands.

“The phenomenon is governmentwide,” said Stier, “but it is a much starker and scarier proposition when it relates to the capacity of government to protect us. That challenge has become so much more acute and sharp.”

After the blush of patriotism that followed Sept. 11, the federal government has had a difficult time finding enough people with the right abilities or education for national security jobs.

The Homeland Security Department has had particular recruiting problems, exacerbated by the reputation it has gained as a bad place to work. It ranked second from the bottom in a private survey of employee satisfaction this year — only the Small Business Administration did worse.

Homeland Security is supposed to be hiring 10,000 new Border Patrol agents between 2005 and 2010, at a rate of 2,000 a year, but has fallen behind. At a hearing in June of a House Homeland Security subcommittee, Republican Mike D. Rogers of Alabama said fewer than 2,000 new agents are “on board,” not including another 1,250 who are in training.

The chairman of the House Homeland Security Committee, Bennie Thompson of Mississippi, said it doesn’t appear that the department has spent sufficiently on recruiting. But a fellow Democrat on the panel, Christopher Carney of Pennsylvania, pointed out that the increase in the Border Patrol authorized by the 2004 intelligence law has not been followed with year-to-year appropriations for all of the new people.

Border Patrol officials say only that they are not having trouble finding quality job candidates.

A union that represents some Homeland Security employees contends that higher pay would help a lot. In the San Diego area, for example, the local police departments pay significantly more than the Border Patrol, John Gage, president of the American Federation of Government Employees.

For the Army, the Iraq War, which is now into its fifth year, remains the major contributor to recruiting challenges, said Rep. Vic Snyder, an Arkansas Democrat who sits on the House Armed Services Subcommittee on Military Personnel, which he chaired until recently.

“When families sit around the living room and talk about whether a young person should go into the military,” Snyder said, “a lot of parents and grandparents out there are not very excited about seeing their young people off to Iraq.”

Financial incentives, lower standards and an increase in the number of recruiters A-— sometimes paid civilian contractors — have enabled the Army to meet or come close to its quotas for the past four years, but the strain is telling. The Army fell short of its goals in May and June by a total of about 1,800 soldiers, which does not bode well for the future.

Jeffrey L. Spara, the Army’s recruiting chief for enlisted soldiers, said that the year-to-date numbers are still ahead of 2006, but “the rest of the year looks like it’s going to be tough,” and he does not expect a turnaround before 2009. There are many reasons for that, he said, among them a greater percentage of high school graduates who are going straight to college and a pool of potential recruits that’s shrinking. Only about one in three youths is fully qualified to join the Army.

The recruiting problem for civilian federal agencies is more selective. The FBI’s glamour, for instance, makes it a major draw for applicants: 374,000 tried to join in the previous fiscal year. But “getting in the right people is the first priority, sorting through the 374,000 and picking the right skills out of that,” said the agency’s chief human resources officer, Donald E. Packham.

Intelligence agencies also have more applicants than they can hire. “Our mission is a very powerful magnet,” said Sanders at the Director of National Intelligence’s office. But not necessarily the right kind of applicants are attracted.

The intelligence community, for instance, faces serious obstacles in boosting its number of linguists, particularly for languages spoken in the Middle East and Central Asia.

The House version of the fiscal 2008 intelligence authorization bill calls for more funding for language training and capabilities, although the exact amount is classified. Michael Morrell, an associate deputy director of the CIA, said the search for linguists is made more difficult by the fact that only 2 percent of the population in the United States speaks the languages deemed a high priority, such as the Urdu of Pakistan or the Pashto of Afghanistan.

Finding specialists is also a problem for other components of the federal government that deal in national security. The armed services, for instance, have a shortage of doctors. “On the medical professionals side, it is a challenge to compete with the world, frankly,” said Lt. Col. Paul L. Aswell, the chief of the Army’s officer division.

Even finding people who want to lead these national security agencies has sometimes proven difficult.

After Michael D. Brown, a Bush presidential campaign fundraiser whose top managerial experience had been as an official of the International Arabian Horse Association, was forced out as director of the Federal Emergency Management Agency (FEMA) following the Hurricane Katrina disaster, several candidates turned down the opportunity to replace him. They cited reasons ranging from concerns that the post was not viewed as being valued by the Bush administration to a preference for their current jobs.

“I wanted to make sure that there was a true 100 percent commitment by the administration that FEMA was going to be” a priority, said Ellen M. Gordon, Iowa’s former emergency management director, in an interview last year. “I didn’t want to be part of something that wasn’t a priority.”

According to a report released this month by the House Homeland panel, 24 percent of the Homeland Security Department’s leadership posts are vacant this summer.

The position of top deputy in the Office of the Director of National Intelligence has been vacant for more than a year, and only this summer did the president nominate Donald Kerr, head of the National Reconnaissance Office, to take the post. Michael McConnell, who since January has been Director of National Intelligence, or DNI, an arm of the White House — turned down the top deputy’s job himself when he was approached about it last year, reportedly because he wasn’t interested.

Filling those leadership positions with the best talent is crucial to drawing in and keeping employees at the lower levels. “Once talent gets into the government, it is often not managed in such a way that the talent wants to stay, or [is] motivated to give its very best,” said Stier. “Federal employees don’t believe they’re getting the leadership they need.”

The federal government frequently is beaten out by the private sector in competition for job candidates. “That leaves the federal government with more people who are security- and compensation-focused,” said New York University professor Paul Light, an expert on the filling of top executive branch positions. “That’s not the kind of employee you want.”

Once new national security personnel are recruited, training them well and even getting them into their jobs can be complicated and time consuming, causing some recruits to move on.

One Egyptian-American woman, who is a senior intelligence analyst, spent nearly a year and a half waiting for a security clearance. Her language skills and education made her an attractive candidate for an intelligence job, and she had a powerful motive to join: She had once worked in the World Trade Center. But the clearance process was grueling. She said she had to produce documents about her mother’s citizenship, for instance, even though her mother was deceased, adding weeks to the process.

“It was a difficult and unnecessarily long process because there wasn’t much sense in what was being asked,” said the official, who declined to be named because of the classified nature of her work. “You just hang out and wait for them to say ‘green light’ or ‘red light.’ ”

The Office of Personnel Management has made progress in reducing what had become an embarrassing backlog for security clearances, but the DNI’s Sanders said, “I still worry about how long it takes to hire and clear people.

“We get people who want to work for us so much, for the most part, they’re willing to wait it out,” he said. “We ought not make it worse with self-inflicted wounds.”

At the State Department, the application process, with its Foreign Service exam, takes about a year, sometimes longer.

Training new hires comes with its own problems. At the FBI, Packham said he is suffering from a shortage of qualified training instructors. The Senate Intelligence Committee, in its report on the fiscal 2008 intelligence authorization bill, said the FBI’s counter–terrorism plan does not lay out a clear training agenda.

“Our limitation on hiring people,” Packham said, “is our ability to get them through training.”

Sanders said the pool of language trainers in intelligence is likewise small. It takes between five and seven years to fully develop an intelligence analyst, he said, meaning that the new generation of people hired right after Sept. 11 are only now beginning to come into their own.

The Senate Select Intelligence Committee has recommended that intelligence agencies delay personnel increases until they have a plan for managing the growth. The committee is concerned “that our training pipeline can’t absorb them,” Sanders said. “That’s legitimate, but let’s get them on board now so they’re in place in three, five, seven years.”

Training can be costly, too. The Homeland Security Committee has found that the cost of recruiting, training and equipping a single border agent can reach $190,000.

When Rogers, at a committee hearing in 2005, asked Thomas Walters, the agency’s head of training and development, why it cost more to train a Border Patrol agent than it did to send someone to Harvard to earn an undergraduate degree, he replied that the government’s expenses included recruiting costs as well as the price of a pistol, a computer, uniforms and leather, one-third of the expenses of a patrol car, as well as a share of the cost of local office space.

Ineffective training can be dangerous. In 2003, the Homeland Security Department’s inspector general found that it was too easy to sneak deadly weapons onto airplanes and blamed airport screeners’ poor training. Follow-up investigations determined that in some cases, screeners did not get the required three hours of training each week.

NYU’s Light said that, too often, the federal government undervalues training. Stier said there was a direct correlation between rising employee satisfaction at the State Department and training. From 2003 to 2005, Secretary of State Colin L. Powell invested heavily in training, Stier said, and employees responded well.

Union president Gage contends that morale problems at Homeland Security have deepened because training seems like an afterthought. One border agent Gage met told him he was asked to enlist in a training class even though he would soon retire. The manager sent him anyway to meet a quota.

Holding on to trained, experienced personnel is a perennial problem for the military and other federal agencies, and retention rates are eroding because of the long hours of government service, the high risk of some jobs or the lure of the private sector.

Like all federal agencies, those that focus on national security also face a wave of baby boomer retirees who will be lost no matter what. What the agencies want to avoid is resignations. “We invest a lot of money training them,” said Sanders. “To get a full return on that investment, we need to do a lot on retention.”

Carney, a counterterrorism expert and college professor who briefed Pentagon officials on the relationship between Iraq and al Qaeda in the months before the Iraq War began, was named as a freshman this year to chair House Homeland Security’s Management, Investigations and Oversight Subcommittee.

That panel held a hearing June 19 that delved into reports that the contractor DynCorp, hired by the State Department to train Iraqi border guards, had recruited heavily among U.S. border security agents. Private security contractors also have vacuumed up airport screeners. Carney said: “Once a screener stays long enough to get valuable experience, they leave.”

Airport screeners who lift and move baggage also suffer the highest civilian rate of injuries in the federal government, which contributes to the departure rate.

The FBI has lost six leaders of its counterterrorism division since Sept. 11. The previous holder of the job, Gary M. Bald, left last year for a job with Royal Caribbean Cruise Lines. While Packham said the turnover among FBI leaders is no worse now than at any other point in its history, Bald’s departure was the final straw in a series that frustrated Congress and the director of the FBI, Robert S. Mueller III. Mueller, who blamed long hours and the private sector’s salaries for the numerous departures, asked for a longer commitment from Bald’s replacement, William T. Hulon.

Morrell said the CIA loses more employees to retirement than resignations for the private sector, but the 100 to 200 he estimates he loses each year — usually the more experienced employees — are generally not the ones he’s happy to see depart.

Given the enormous demand for national security personnel and the accompanying struggles in hiring, training and keeping them, the federal government has employed solutions that range from innovative to controversial, to both.

The Army has made greater use of waivers for recruits with medical problems and criminal histories as a way of making up recruiting shortfalls.

“You don’t want to take away the ability to do these kind of waivers,” said Snyder. “But you start hearing of some individual cases where this is probably not helpful to the military or the new recruit.”

Shortfalls also have contributed to recruiting shortcuts, he said, pointing to a case in Tennessee where recruiters urged prospective soldiers not to disclose mental health problems. Snyder said fewer Army recruits have graduated from high school, with the percentage falling by more than 10 percent in two years. “The trend is concerning, although those may turn out to be fine soldiers,” he said.

The Army’s Spara said the service reflects society. The percentage of high school graduates is on the decline, for instance. He said the Army closely reviews cases of recruits with criminal backgrounds, and he has not noticed a spike in recruiting scandals.

Faced with shortfalls or outside limitations on their numbers, the Pentagon and intelligence agencies are making more use of contractors. That, in turn, has set up competition for labor and can raise the cost of services to government.

Reliance on contractors raises questions about what roles the federal government should let the private sector play. The use of contractors for interrogating military prisoners, for example, has been controversial. That reliance has led to an intelligence-communitywide review of how many contractors are working in spy agencies and what can be done to reduce their numbers. The House and Senate Intelligence committees have also sought reports on the number of contractors.

The CIA, which is reviewing the roles contractors perform, has in the meantime decided to cut its number of contractors by 10 percent and forbid employees who have resigned from the agency from coming back as contractors for a year and a half, said Morrell.

The new personnel systems at the departments of Defense and Homeland Security were an attempt to modernize how the government hires, pays and fires employees to respond to the immediacy of the terror threat. The intelligence community is working to establish a system that adopts one of the main elements of those new personnel systems: “pay for performance.”

Sanders said employees are not so much worried about the concept of tying pay to performance, but how it would be implemented — common refrains from workers at the other agencies who have said they are concerned about their rights to appeal and whether managers would be properly trained in how to reward good performers.

The Homeland Security and Pentagon systems have been challenged successfully in court. In addition to pay for performance, both systems would limit collective bargaining.

The Partnership for Public Service’s Stier said there is value in the pay-for-performance model, but that collective bargaining rights have been a distraction. Light said the ultimate result of the Homeland Security and Pentagon systems is that they have confused and slowed the hiring process.

The intelligence community has adopted other tactics that could point the way for security agencies in general.

McConnell’s decision as national intelligence director to remove obstacles to hiring first- and second-generation Americans has been widely praised, for instance.

The intelligence community and other agencies with national security missions have also made heavy use of incentives such as college loan repayments. Spy agencies and the military have made effective use of scholarships to recruit specialists such as linguists and medical personnel.

“In today’s world, many of our most talented have debts that preclude them from making the public service choice,” Stier said. “It’s more effective to address that debt issue than to pay a top salary.”

And McConnell is leading an effort to speed the security clearance process by completely overhauling it, citing the ease with which automated records checks in the private sector turn control of billions of dollars worth of financial transactions over to employees who pass such background checks.

For now, though, the personnel challenges span the government’s entire security apparatus. “Whether it’s the Border Patrol or intelligence analysts at the CIA, you have substantial talent needs the government is going to have to fill,” Stier said. “Throw a rock, you find a problem.”

Fiscal 2008 Intelligence authorization bills (HR 2082, S 1538, CQ Weekly, pp. 1768, 1443; Homeland Security authorization (HR 1684), p. 981; McConnell, p. 880; Pentagon problems, 2006 CQ Weekly, p. 3275; FBI problems, p. 1155; intelligence overhaul (PL 108-458), 2004 Almanac, p. 11-3; Homeland Security Department’s creation (PL 107-296), 2002 Almanac, p. 7-3.