CENTRAL ISLIP, N.Y. » The former chief of one of the country’s largest local law enforcement agencies was arrested today on charges he took revenge against a man who broke into his SUV by beating the suspect at a police station.

Former Suffolk County Police Chief James Burke was arrested by federal agents at his Long Island home to face charges of violating the man’s rights by assaulting him and of conspiring to cover it up. He was awaiting an afternoon court appearance.

U.S. Attorney Robert Capers said Burke influenced officers in his department to lie about what happened inside the police station. The prosecutor told reporters to “stay tuned” on whether further arrests were possible.

Burke’s attorney, Joseph Conway, denied the allegations and said Burke looks forward to his defense.

Burke had been under scrutiny for years over an allegation that he beat a prisoner in 2012. He resigned from the force in October.

Suffolk County Executive Steve Bellone, who appointed Burke in 2012, confirmed in October that Burke’s departure was related to a renewed federal investigation.

Burke initially was investigated by the FBI in 2013 on suspicion that he may have abused a man suspected of stealing a gun belt, ammunition and handcuffs from his department issued vehicle.

Christopher Loeb had been arrested after someone broke into the chief’s department-issued SUV. Loeb later pleaded guilty to a weapons charge.

Loeb, who has filed a civil rights lawsuit against Burke and the department, claims he was assaulted initially at his home by officers and subsequently at the precinct, where he said he was beaten by Burke and other officers.

Loeb’s attorney, Amy Marion, said in a statement that her client will continue to cooperate with investigators. “We are gratified that this long overdue prosecution has begun and we look forward to seeing that justice is done,” she said.

Before Burke was named chief, he worked as an investigator for the Suffolk County district attorney.

The Suffolk County Police Department, with more than 2,000 officers, is among the country’s 15 largest departments. It has responsibility for patrolling much of eastern Long Island, although the Hamptons and several other towns also have local police departments that patrol those areas.

Burke’s October resignation was followed last month by the retirement of Police Commissioner Edward Webber. Several other top-ranking officers, including the chief of detectives, also have retired in recent weeks.