Appropriately enough for start of a new baseball season, Bob Mueller got a little “chin music” last week from the Senate Judiciary Committee, which wanted to send him a message over who’s really in charge of his FBI.

Mueller had to duck a number of high and tight fastballs from both Republicans and Democrats, who were seething over the FBI’s failure to keep track of perhaps hundreds of thousands of warrantless subpoenas served secretly on American citizens, businesses and organizations since 2001.

The FBI had been warned by lawmakers to carefully manage the immense power given it by the USA Patriot Act, which allows bureau supervisors to issue so-called national security letters that prohibit its recipients from telling anyone they had gotten one. (The law has been amended to permit recipients to tell their lawyers—but no one else.)

Patrick J. Leahy of Vermont, holding the gavel as the panel’s new Democratic chairman, saw the latest flap as emblematic of the FBI’s failure to transform itself into a law-abiding secret police outfit.

“Almost six years after the September 11th attacks,” he said, “it troubles all of us that the FBI has not yet lived up to its promise to be the world-class domestic intelligence agency the American people expect and need it to be.”

“The learning curve has gone on too long,” he lectured Mueller. There were growing calls “to take away the FBI’s domestic intelligence functions [and] create a separate domestic intelligence agency, like Britain’s MI5.”

But it was Arlen Specter, R-Pa., the intense, five-term former Philadelphia prosecutor, who really came at Mueller.

At 77, Specter has weathered a brain tumor, heart disease, cancer and the loathing of right-to-life Republicans. On Tuesday, March 27, in the Judiciary Committee’s high-ceilinged hearing room he threatened to take the bat out of the FBI director’s hands — an unimaginable tack during the 50-year reign of J. Edgar Hoover, who came to the Hill armed with his private files on senators’ peccadillos.

“Every time we turn around,” Specter lectured Mueller, a former federal prosecutor himself, “there is another, very serious, failure on the part of the bureau.

“We had the inspector general in last week, went over three of the inspector general’s reports. And they present a picture [that produces a ] lack of confidence, to put it mildly.

“On the national security letters, the inspector general found, quote, ‘widespread and serious misuse of the FBI’s national security letter authorities.’ The oversight was inconsistent and insufficient.

“Then, within the past 45 days, a report on the issue of terrorism reporting. The inspector general concluded, quote, ‘The collection reporting of terrorism-related statistics within the department is haphazard.’

“Then, on the issue of weapons and laptops — quote, ‘The FBI could not determine in many cases whether the lost or stolen laptop computers contained sensitive or classified information.’ ”

Spector shifted in his seat, looking almost like he’d like to reach down over the dais and swat Mueller on the head.

He, too, said amputating the FBI’s domestic counterintelligence and giving it to a new agency could well warrant “very serious deliberation by this committee. We have authorities lined up on both sides. But there are sufficient problems that I think it needs to be considered.”

In reality, there’s little stomach today for creating yet another army of domestic spies.

The MI5 idea rose with the smoke of the Sept. 11, 2001, attacks and evaporated amid furious FBI lobbying that it could handle the job.

There’s “no serious discussion regarding MI5 that I am aware of,” said one close observer with solid intelligence credentials. But if al Qaeda gets through again, “the first piece of legislation to be passed will establish a U.S. MI5-like organization as a solution to current failures.”

In the meantime, evidence keeps piling up that the bureau can’t handle the strain.

The same day Mueller came to the Hill, The Washington Post reported that hundreds of millions of dollars had also gone awry in a Justice Department program to develop a secure wireless communications system with DHS, the latest chapter in a sorry FBI record on technology upgrades.

The Bureau’s applications for wiretaps were also full of mistakes, it turned out.

“How can it be that your highly trained agents make so many factual mistakes?” Specter asked Mueller.

The well-groomed former Marine waffled.

“The affidavits are exceptionally long,” he said amid a verbal cloud. “You can have thousands of facts in there.”

“Director Mueller,” Specter said, “I’m not impressed by your assertion that there are thousands of facts. That’s your job. That’s the FBI agent’s job.”

Specter marvelled at the string of management scandals at the FBI, that “another shoe drops, virtually on a daily basis.”

“Director Mueller, this committee has enormous respect for you, and I have enormous personal respect for you,” Specter offered. “The question arises as to whether any director can handle this job. And the further question arises as to whether the bureau itself can handle the job.”

Members of the House Select Intelligence Committee, meanwhile, seemed equally astounded that the FBI had issued over 140,000 national security letters between 2003 and 2005 with so little discernable impact.

The haul, as far as they could determine from the auditors’ report: one conviction for the material support of terrorism. Another 152 “criminal proceedings” were attributed to the NSLs.

“So considering that, how effective are these?” asked Rep. Anna G. Eshoo, D-Calif., a friend of Speaker Nancy Pelosi, D-Calif.

Suddenly, the spectre of Mueller’s FBI morphing into a national laughingstock along the lines of Tom Ridge’s Homeland Security Department seemed real.

Even Peter Hoekstra, the loyal Michigan Republican who ceded the Intelligence Committee gavel to Silvestre Reyes, D-Texas, in January, seemed nonplussed by the surprises that federal auditors and the press kept discovering at the FBI.

“This is yet another manifestation of what I believe is a constant and unacceptable failure of this administration — and I will stress ‘this administration’ — to fully report intelligence programs and activities to Congress,” Hoekstra fumed

“There is a pattern here, which I find very disturbing, that I’ve experienced over the last two and a half years.”

Most weekends I play golf with a former top FBI intelligence official. Mostly we complain about our hooks and slices and bad putts.

But last weekend we couldn’t resist shaking our heads over news that senior FBI managers had ignored the warnings about the national security letter mess from one of their own agents — for three years.

“This is not the FBI I recognize,” he said.

What I think he meant was that his post-Watergate FBI made plenty of mistakes, but under the leadership of Judge William Webster, in particular, it went a long way toward regaining respect as a principled, law-abiding organization.

Mueller, by contrast, can’t seem to rid the bureau of some of its old, bad habits.

Stories of FBI managers resisting his reforms, cutting corners and punishing rank-and-file agents who blow the whistle on them seem to have proliferated since 9/11.

Iowa Republican Sen. Charles E. Grassley asked Mueller about just two of over a dozen cases.

One involves former Special Agent Mike German, who spent most of his 16 years in the FBI penetrating domestic hate groups.

German advised his bosses in 2002 that the mishandling of a clandestine recording of foreign terrorists and white supremacists agreeing to a domestic anti-Israel alliance could jeopardize future prosecutions.

His bosses’ solution was to falsify documents, lie to Justice Department investigators and harass the decorated agent into quitting the bureau.

“I e-mailed Mueller when this first developed in January 2003,” German told me last week, “and said you need to pay attention to this because it’s going to embarrass the bureau.”

It did, but not enough, evidently, to warrant any action on Mueller’s part.

“These facts are disturbing,” Grassley told Mueller, “but even worse is that the FBI seems more interested in protecting itself than in developing some human intelligence on extremist groups. An FBI spokeswoman even went on television to deny that the groups discussed working together. The FBI also claimed that the subjects did not discuss terrorism.”

But “after a long struggle,” Grassley announced, “this committee finally obtained this transcript I’ve referred to of that meeting directly from the FBI. The transcript repeatedly contradicts the FBI — what the FBI said — and supports what Michael — Special Agent Michael German said.”

“[T]hey talk about their shared admiration for Hitler, arms shipments from Iran, their desire for a civil war in the United States, and their approval of suicide bombings,” Grassley continued, “and lastly, assassinating pro-Israeli journalists in the United States. This is all in their very first meeting with each other.”

Grassley peered down at Mueller and threw a rhetorical fastball at his head.

“Can you explain why the FBI didn’t jump at the chance to infiltrate these organizations instead of wasting the time retaliating against Special Agent German?” he asked.

Mueller kept his cool.

“My understanding,” he replied, “is that the inspector general’s investigation found no missed opportunity in that set of circumstances. But I’ll have to go back and look at that, and get back to you, Senator.”

As it turned out, the internal warnings about problems with the warrantless subpoena programs had come from Bassem Youseff, once the FBI’s top Arab-American counterterrorism agent, who had been passed over for a promotion in favor of less qualified agents after the 9/11 attacks.

Sidelined in the Communications Analysis Unit, Youseff sued the bureau. (It was his lawyers who took the infamous 2005 video depositions of top FBI officials, including Mueller, in which they admitted they knew nothing about Sunnis and Shiites and could not care less.)

Grassley asked Mueller about several hundred “exigent letters,” an even more urgent tool the FBI uses, “to obtain phone records without issuing a subpoena or following the statutory process for the national security letters.”

“Those exigent letters contain false statements,” Grassley said, “and we need to figure out whether the FBI supervisors signing them knew that they were false.”

“Why weren’t we able to get those e-mails before this hearing, and when will we be receiving them?” he asked Mueller.

“I’d have to get back to you on the timing of when you’ll receive them,” answered the director.

I have another friend in the FBI who I asked about the fuss as Mueller trudged to the Hill last week.

“Ridiculous!” he shouted.”It’s about records! Record keeping!”

The FBI, he noted, has been getting people to turn over records without subpoenas forever.

“Just like on TV, we tell them we can be back with a subpoena from a U.S. Attorney in 10 minutes, so they might as well spare the effort.”

If a lawyer moves to quash the FBI’s demand for records, the Justice Department goes to a judge.

Same result, almost always.

The so-called FISA court (set up by the 1978 Foreign Intelligence Surveillance Act), also emits subpoenas like Metrorail cards.

But people have to give the FBI a little trust in these dangerous times, said my friend, a ranking counterterrorism official.

“FBI agents don’t wake up in the morning wondering how they can violate somebody’s constitutional rights,” he sputtered. “They’re trying to prevent another terrorist attack, not bust their rinky-dink antiwar group.”

Suggestions to the contrary, he said, throw dirt on the work of thousands of skilled, dedicated agents and supervisors who stay awake at night worrying about the next al Qaeda plot.

Yes, he conceded, management should have done a better job keeping track of the national security letters. But he says it’s no big deal and that the FBI is busy chasing terrorists, not us.

Americans should just ignore the headlines and relax.

“Hoover is dead, fer crissakes!”

Jeff Stein can be reached at jstein@cq.com.

Niger Update: Rep. Henry A. Waxman, D-Calif., last week dialed up the heat on Secretary of State Condoleeza Rice, requesting her presence for an April 18 hearing of his Committee on Oversight and Government Reform to explain on the administration’s use of fabricated Niger uranium documents to push the nation to war in Iraq. No response yet from State. A dozen letters Waxman sent Rice when he was in the minority went unanswered. . . .Speaking of Nigergate, something on that from last week’s column needs clarifying: The CIA never got originals of phony documents from SISMI, Italy’s military intelligence service, in Feb. 2002, purporting to show Saddam Hussein’s purchase of Niger yellowcake to make nuclear bombs; it got a verbatim copy of the text. Still, write Peter Eisner and Knut Royce, authors of “The Italian Letter,” a new book on the affair, the errors in the text were so obvious that the bogus “intelligence” should never have made it into the White House, much less into President Bush’s now infamous 2003 State of the Union speech.

More Secrets of State: A March 9 press release from State’s Bureau of International Organization Affairs mourned the death of “our colleague and friend, Clarence B. Winder . . . who passed away on Monday, March 5, 2007.” Actually, according to reliable sources, Winder committed suicide, another casualty, one of the sources contended, of “uncaring management practices” at the State Department. “Wednesday he was found in his home, dead of a self-inflicted gunshot wound.”

On Friday, March 30, career Foreign Service Officer Bruce Knotts resigned. writing that the “suicide of a colleague tipped the scale” in his decision to join a parade of diplomats forced to leave State because their security clearances had been arbitrarily lifted. In a letter to Condoleeza Rice, Knotts compared today’s exodus to the 1950s-era State Department’s purge of liberal dissenters, and charged that the State Department’s Bureau of Diplomatic Security “has once again begun using an open-ended political war, this time the War on Terror, as a similar cover to once again attack gays, lesbians and others it doesn’t like.”

Hastings Exit: Judicial Watch, which put notches on its gun hounding President Clinton into impeachment over Monica Lewinsky, now has its sights on Rep. Alcee L. Hastings, D-Fla., who quietly resigned as chair of the House Intelligence Subcommittee on Oversight and Investigations earlier this month. Once Speaker Nancy Pelosi’s pick to chair the whole committee, “Hastings simply realized he could not devote enough time to chairing the subcommittee and the Helsinki Commission,” an independent federal agency that monitors human rights, according to a March 21 story by my CQ colleague Tim Starks.

Judicial Watch filed suit against Hastings last week, charging that the Florida congressman, an impeached former federal judge, “violated federal law by attempting to improperly terminate the employment of our client, Mark Milosch, and three other employees of the Commission on Security and Cooperation in Europe (also known as the Helsinki Commission).” JW says it’s seeking a temporary injunction to stop the firing of Milosch, the commission counsel.

A Hastings statement March 30 said that Milosch was “hired by Republicans well after the American people swept them from power last November” and “was never hired consistent with the law in the first place.”

“I have litigated against better,” Hastings said, “and will prevail in this case. This is simply much ado about nothing.”