PORTLAND — FBI officials said Monday that Boston-area operations, including Maine, could be affected by budget cuts under federal sequestration.

Vincent Lisi, newly installed special agent in charge at the FBI’s Boston office, said at a meeting with Maine news media that the agency must “write a check” back to the federal government for more than $700 million, a daunting task considering most of the agency’s budget, roughly 68 percent, is payroll.

He said the across-the-board budget cuts that automatically took effect earlier this year have “rippling effects” that “are tremendous.”

For the FBI, that means not only a hiring freeze, but retiring agents wouldn’t be replaced, Lisi said.

In Maine, there are 14 agents who work out of offices in Portland, Augusta and Bangor. Attrition could lower that number if the sequester were to continue through next year, said Aaron Steps, the FBI’s senior supervisory resident agent who oversees Maine operations.

If agents were assigned to help state and local law enforcement to combat pharmacy robberies in Maine, for example, they might have to pull those agents off that detail if a terrorist threat were to occur at the same time, said Steps, also new to his job this year.

Although white-collar crimes comprise the greatest portion of FBI investigations in Maine, prescription drug abuse likely has had the greatest impact on the state, Steps said, calling the statistics “absolutely astonishing.”

Lisi also said agency workers would likely be furloughed for up to two weeks in the next fiscal year if the sequester continues. He said he hasn’t figured out how to do that without affecting ongoing operations.

“Does the FBI shut down for a day?” he asked rhetorically. “Now you have a national security threat as well, because if the FBI’s going to shut down, then what happens? Obviously if something bad happens, if there’s a terrorist attack, we’re going to respond. But from where?” That could result in a delayed response, he said.

The combined effects of reduced staff could force the agency to pick and choose among its programs and investigatory efforts.

As that happens, “We lose the ability to pursue certain threats out there,” Lisi said. Operations would be prioritized and efforts allocated accordingly, he said.

Steps said Maine’s vast geography poses a unique challenge to his limited staff. His agency is working more than ever to join forces with state, county and local law enforcement. Several task forces in the state combine resources. The agency also has formed partnerships with non-law enforcement entities.

“We realized a long time ago we can’t do it alone,” Lisi said.

U.S. Attorney Thomas Delahanty II, who attended Monday’s meeting, said his office has felt pain from the sequester as well as from the shutdown of the federal government.

Although he hasn’t lost any attorneys yet, he has lost support staff, which has slowed paperwork that flows through his office which handles prosecution of federal cases in Maine. As long as the sequestration continues, retiring attorneys and their assistants at his office won’t be replaced.

Congress recently returned to work on the sequestration issue. It appears the initial hope of replacing the sequestration cuts with a comprehensive plan has been altered to a more modest and practical goal of replacing the across-the-board cuts with more deliberate cuts.

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