The former chief of the Suffolk County Police Department will remain behind bars, as a judge has refused to grant him bail. U.S. District Judge Leonard Wexler said of James Burke, "The corruption of an entire department by this defendant is shocking."

Burke was arrested on Wednesday and indicted for deprivation of civil rights and conspiracy to commit obstruction of justice. The Eastern District U.S. Attorney's office alleges that in December 2012, Burke interrupted the interrogation of Christopher Loeb, who had broken into a number of vehicles, including Burke's department SUV: "Burke entered the interrogation room where Loeb was handcuffed and chained to an eyebolt fastened to the floor. Burke then allegedly punched and kicked Loeb in the head and body."

Besides stealing Burke's gun belt, ammunition, some cigars and a humidor, Loeb took a duffel bag that apparently held pornography and sex toys. Loeb thought the porn was kiddie porn, and allegedly called Burke a "pervert," which prompted the assault. Court papers state, "Knowing Loeb was a heroin addict, Burke threatened to kill Loeb stating that he would make sure Loeb received a 'hot shot,'" a.k.a. a lethal injection.

Loeb was in custody for days and was unable to contact his lawyer.

The feds also say that Burke bragged about beating Loeb and "regaled a group of officers with his account of the assault, saying it reminded him of his 'old days' as a young police officer." He is also accused of asking the officers who witnessed the beating to downplay the attack, and prosecutors say, "Knowing Burke's reputation for violating the law and seeking retribution against those who went against his corrupt orders, the witnesses feared their careers would be destroyed if they did not join Burke's conspiracy to cover up the assault of Loeb."

The AP notes, "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 ritzy Hamptons and several other towns also have local police departments that patrol those areas."

Burke is being held in protective custody at the Metropolitan Detention Center in Brooklyn. His attorney said, "We are going to appeal. All the alleged cooperators have a reason to testify against Mr. Burke."

Loeb's lawyer told PIX 11, "He doesn't have a feeling of security, of being safe. He was very, very scared and he still is." Besides the alleged beating from Burke, Loeb has said that Detective Anthony Leto choked him and threatened to rape his mother. Leto and other officers tied to the incident retired last month.