Former Suffolk County Police Chief James Burke was arrested and charged in a two-count federal indictment Wednesday stemming from an alleged assault in 2012.

Burke, 51, is facing deprivation of civil rights and conspiracy to commit obstruction of justice charges. He has been under federal investigation after allegedly assaulting a Smithtown man who was arrested for stealing Burke's bag from his police SUV.

Federal prosecutors say Burke drove to Loeb's house after he was identified as the suspect to retrieve his bag. He then allegedly "punched and kicked Loeb in the head and body" after he was taken to a nearby precinct. Prosecutors say Burke, "together with other members" of the Suffolk County Police Department, tried to cover up the assault.

"Defendant Burke repeatedly met with members of the Suffolk County Police Department who had witnessed Burke's assault on Loeb to agree on ways to get their story straight," says prosecutor Robert L. Capers.

Prosecutors asked for no bail for Burke, calling him a "danger to the community." The feds allege in a letter to the judge that Burke also threatened Loeb's life by saying he would give him a fatal dose of heroin.

Defense attorney Joseph Conway says Burke never threatened Loeb and that the charges won't stand up in court.

"We contest these things even happened... We don't believe the government will be able to show Mr. Burke is a danger on an ongoing basis," says Conway. "This obviously is a tarnishment to his career and he will vigorously defend himself."

Burke is being held in protective custody until his bail hearing on Friday. If convicted, he could face more than five years in prison.