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CENTRAL ISLIP, N.Y. — The disgraced former chief of the eighth largest police department in the country is now in federal custody, and for now, he’s not permitted to post bail.

It’s the latest development in a case of the alleged torture of a prisoner who’d been in the custody of James Burke when he was chief of the Suffolk County Police Department three years ago, and a conspiracy to cover it up.

Burke, 51, retired from his position as chief last month in the wake of a federal probe.  On Wednesday, however, he went from being the former commander of Suffolk County Police Department to an accused criminal.

Around 6:00 a.m., FBI agents put Chief Burke into handcuffs on his front lawn in the village of St. James.  They continued to transport him to the FBI office in Melville, and then to federal court here, where federal prosecutors announced charges against the veteran law enforcement officer.

Burke is charged with “assaulting and thereby violating the civil rights of a Smithtown man arrested for breaking into Burke’s department-issued vehicle and stealing his property on December 14, 2012,” U.S. Attorney Robert Capers announced in a statement.  “Burke is also charged with conspiracy to obstruct a federal civil rights investigation into the assault,” the statement said.

That Smithtown man is Christopher Loeb, 28.  In December 2012, Loeb broke into cars, including the unmarked police SUV assigned to Chief Burke.  Loeb stole a duffel bag from Burke’s vehicle.  Inside were a police gun belt, ammunition, handcuffs and what prosecutors call, in their indictment “other items.”

Loeb has called those items, on the record, “nasty porn.”  It’s what Loeb also called them to Chief Burke’s face, when the chief showed up at Loeb’s home the night he was arrested.  “That’s a highly unusual situation for any chief to be in,” said U.S. Attorney Capers at a news conference Wednesday afternoon.

Capers’s office also submitted a sealed memorandum to the judge in the case, Leonard Wexler, saying that Burke is a danger to the public and specifically to Loeb, and therefore should not be granted bail.

According to Newsday, the memorandum said that Burke had threatened to give him a “hot shot” of heroin, the slang term for an overdose, while Loeb was in custody for days after his arrest, without access to an attorney.

Loeb now has a lawyer, who told PIX11 News that Burke’s threatening message went far beyond the night of the arrest.  “He doesn’t have a feeling of security, of being safe,” said Amy Marion, Loeb’s attorney.  “He was very, very scared and he still is.”

Loeb served two years in prison for the car break-ins and thefts, but since he’s been out from behind bars for more than half a year, he’s been followed repeatedly, Marion said, and generally felt threatened by Burke’s associates.  Loeb has a civil case against Burke and the Suffolk County Police Department also pending.

Because of the concern of Burke harming others, prosecutors asked that Chief Burke remain behind bars with no bail pending trial.  For now, they’ll get their wish, until a closed bail hearing on Friday.

“We contest that these things ever happened,” said Joseph Conway, Burke’s attorney, regarding the allegations that the chief threatened Loeb’s life. Conway said that he’ll ask the judge, in a closed hearing on Friday, that his client “should be released.”

Burke entered a plea of not guilty at his arraignment Wednesday afternoon.