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CENTRAL ISLIP, N.Y. — When recently retired Chief of Department, James Burke, appeared in handcuffs with FBI agents Wednesday, the Suffolk County Police and other law enforcement knew the FBI wasn’t finished with its investigation.

It may be just the beginning.

Burke is charged with violating the civil rights of a Smithtown man, by beating him—after Christopher Loeb was arrested for breaking into Burke’s department vehicle in 2012—and stealing Burke’s bag, which contained not only a gun and ammunition—but also sex toys and porn.

PIX11’s James Ford followed the investigation into the beating for more than two years, which culminated in Burke’s arrest Wednesday.

Federal prosecutors were apparently able to “flip” police witnesses, who may have lied initially about what they saw inside the Fourth Precinct.

Burke faces a second federal count of conspiracy to obstruct a federal, civil rights investigation.

Burke has a long history with law enforcement, beginning when he was a 14 year old witness in a brutal murder case, involving a 13-year old boy who had stones shoved down his throat in 1979.

The victim was John Pius, and Burke served as the teen witness against other suspects, who were charged with killing Pius, because he witnessed them stealing a mini-bike.

The young prosecutor at the time was Thomas Spota, now the Suffolk County District Attorney.

James Burke was the top investigator in Spota’s office, at one point, before he was recommended for the Chief of Department’s job with Suffolk Police.

When PIX11 contacted Spota’s office Wednesday for comment, we did not receive a response.

Burke has been remanded into federal detention, until his next hearing on Friday.

This case is not the first time Burke was investigated; back in the early 1990’s, he was monitored by Internal Affairs for his relationship with a prostitute.

But he moved on in his career, and his defense attorney, Joseph Conway, said Wednesday of the unsealed, federal indictment “we contest that these things ever happened.”