The FBI’s new special agent in charge of the Boston field office, which covers Maine, led the investigation into the post-Sept. 11 anthrax attacks, was stationed in Yemen after the U.S. Embassy there was bombed in 2008, and helped lead the nation’s counterterrorism efforts out of FBI headquarters in Washington.

But for the challenges facing the nation’s premier law enforcement agency now, it’s his 3½ years of experience as a certified public accountant before he joined the bureau that may be most helpful.

“Sequestration is the biggest challenge,” said Vincent B. Lisi, who has been Boston’s special agent in charge for the past three months.

The budget-cutting agreement that requires across-the-board cuts to most federal programs will result in a $700 million cut to the FBI this year. Personnel accounts for 68 percent of its budget, fixed costs like rent for much of the remainder. Cut training, and agents aren’t as prepared as they should be to do their job, he said.

“We finally realized we’re going to do less with less,” he said, discussing the bureau’s effort to prioritize its missions to focus on the most important, though he would not say what areas might be scaled back.

Lisi introduced himself to the Maine press corps Monday at the office of U.S. Attorney for Maine Thomas E. Delahanty II in Portland along with the resident agent in charge of the Maine FBI office, Aaron Steps.

Steps has been on the job in Maine for eight months.

He previously was stationed in Pakistan and in Nairobi, Kenya, where he lived about two blocks from the Westgate Mall, which was attacked by Somalia-based al-Shabab terrorists last month.

“I would occasionally stop there. When my parents came to visit, we had dinner there,” Steps said. “I was friends with a number of the Kenyans that were working the case. I consider them friends. … It’s very difficult not to be there when that happens.”

Steps said he did not participate in that investigation but the Portland office did have to follow up on the suggestion – later deemed erroneous – that one of the mall attackers was from Maine’s Somali population.

Steps said the need to check the Somali population for information about possible threats was unfortunate but necessary.

“I think for the vast majority of them it’s very painful that this is going on,” he said of the terrorism attacks in that country. “They understand we have to check into it. We try to keep our footprint to a minimum.”

Lisi said the need to respond to such possibilities is one reason it is so important for the FBI to maintain relationships not only with law enforcement agencies throughout the state but with other groups to facilitate communication about potential threats.

Maine’s contingent of FBI agents is relatively small, with 13 agents, not including Steps, spread between Bangor, Augusta and Portland offices, as well as four task force officers assigned to the bureau by police agencies in Maine.

One of the biggest challenges to the bureau here is geography, Steps said. It can take a full day of two Bangor agents’ time to drive to Fort Kent to knock on a door, he said.

Maine has one of the lowest crime rates in the United States, but he said the caseload is proportional to other parts of the country.

“Quite frankly, the biggest impact on the health and well-bing of the people of Maine is prescription drug abuse,” Steps said.

One initiative that is unique to Maine is FBI assistance in investigating pharmacy robberies.

Last year, Maine was hit with more than 50 pharmacy robberies, unheard of in other jurisdictions.

Delahanty, who attended Monday’s meeting, said he requested the FBI’s help in response to the wave of pharmacy robberies.

“It was really an epidemic,” he said, adding that the numbers have dropped this year.

Steps said the FBI agents in Maine also focus on white collar crime, such as financial fraud and health care fraud.

On the national level, as well as in Boston and to a lesser extent Maine, a major focus of the bureau is on counterintelligence.

Years ago, that meant looking for spies other governments may have stationed in the United States, Lisi said. Now, counterintelligence usually entails defending against and investigating cyberattacks.

The bureau’s programming experts work with defense contractors and other high-tech companies researching sensitive technology to make sure their defenses against hackers are adequate. When the FBI learns of a new cyberespionage technique, it alerts businesses that might be targets and works with researchers in academia to make sure the latest innovations are available to important private sector companies, Lisi said.

Lisi takes over for Richard DesLauriers, who was head of the Boston FBI field office during the Boston Marathon bombings and oversaw that investigation.

The Boston office covers Massachusetts, Maine, Rhode Island and New Hampshire, operating joint terrorism task forces in each state.

Lisi said the bureau may explore incentives to have employees retire early to speed up attrition as a way of meeting cutbacks required by sequestration.

A pending retirement in the Maine office won’t be filled, he said.

“The FBI is probably not going to hire another single person for another maybe two years,” he said.

David Hench can be contacted at 791-6327 or at:

dhench@pressherald.com