FBI Director James B. Comey must find $800 million or so in budget savings, out of a total annual FBI budget of about $8.1 billion. (Evan Vucci/Associated Press)

Big budget woes worry the FBI’s new director, James B. Comey, a mere two weeks into the hassle-filled job of a lifetime.

The training pipeline for special agents is empty, curtailed by prior economizing. By Oct. 1, Comey must find about $800 million in savings out of an annual FBI budget of about $8.1 billion. Layoffs and furloughs appear inevitable.

“I’m not playing a game,” Comey told reporters Thursday. “I’m not crying wolf.”

And budget problems are not the only ones to confront the new director since his swearing-in Sept. 4, after a breezy 93 to 1 Senate confirmation vote.

Special agents are scrambling to understand the shooting deaths last Monday of 12 people by a contractor at the Washington Navy Yard. The bureau is facing a scathing new American Civil Liberties Union report into the alleged “unchecked abuse of authority.”

It’s facing heat from the inside, too, as a Justice Department Office of Inspector General report issued Thursday criticized the actions of several FBI field offices.

“One of the challenges of this job is your inbox can come to dominate your life,” Comey said.

Like his predecessor, Robert S. Mueller III, who took office a week before the Sept. 11, 2001, terrorist attacks, Comey identified counterterrorism and cybercrime as the bureau’s top priorities. But shortly before he retired, Mueller acknowledged that his successor would inherit some “hard choices” on the budget.

And it’s the budget that’s really nagging the 53-year-old former federal prosecutor.

“I got briefed on that before I started,” Comey said. “I was very surprised to learn how severe the potential cut is.”

Like other federal agencies, the FBI is handcuffed by a budget mechanism called the sequester. Originally intended by Congress and President Obama as a threat to force tough deficit-reduction decisions, the sequester has instead taken effect and begun imposing automatic across-the-board cuts.

Over the next decade, the automatic cuts are estimated to reduce federal spending by about $1 trillion. Most Justice Department agencies would, like the FBI, shoulder cuts of 8.2 percent.

“It didn’t make sense before I was sworn in, and it still doesn’t make sense to me,” Comey said. “To get to where I need to be, I need to eliminate a bunch of positions, and then we’re faced with a furlough.”

The bureau grew immensely in both staff and funding during the past 12 years under Mueller. In fiscal 2001, it had a budget of $3.3 billion and a staff of about 27,000. By fiscal 2012, the bureau’s budget was $8.1 billion and the staff has expanded to more than 34,000 employees.

Comey said he may have to “cut 3,000 positions,” as well as impose unpaid furloughs of up to two weeks on remaining employees to meet the sequester demands. He declined to spotlight specific programs where the potential cuts might hit.

“I don’t want to talk in particular, because I don’t want the bad guys to know,” Comey said.

Comey will eventually face key administrative decisions. One could be finding a replacement for the brutal-looking J. Edgar Hoover Building, the bureau’s headquarters, on Pennsylvania Avenue.

But it was the Navy Yard mass shooting that was on his mind last week. Comey reviewed videos and met with the FBI special agents who are investigating the incident. While he cautioned that “we’re trying to better understand” the mental status of the slain shooter, Aaron Alexis, Comey said investigators have determined that there was “no connection” to terrorism.

Comey also shed further light on what happened after Alexis entered the Navy Yard on Monday morning, saying that Alexis entered a fourth-floor bathroom carrying a bag and emerged brandishing a cut-down Remington 870 shotgun. When he apparently ran out of shotgun ammo, Comey said, Alexis began shooting with a Beretta handgun he had taken from a security officer he had shot.

“It appears to me he was wandering the halls, hunting people to shoot,” Comey said.

Comey did not discuss the new inspector general report during his hour-long meeting with reporters, but he said he welcomed the criticism leveled by the ACLU in its separate assessment of bureau practices since the Sept. 11 terrorism attacks. In its 69-page report, the civil liberties group blasted the bureau for “a record of extraordinary abuse — particularly targeting racial and religious minorities, immigrants and protest groups under the guise of counterterrorism.”

“It’s good to have that push from the outside,” Comey said. “. . . I’m going to read [the report] with an open mind.”

— McClatchy-Tribune