A former Suffolk County police chief beat up and threatened to kill a junkie who stole a duffel bag containing porn DVDs and sex toys from the chief’s official vehicle — then arm-twisted other cops to cover up the assault, the feds charged Wednesday.

James Burke, who resigned in October, was busted on ­civil-rights and obstruction charges for allegedly assaulting Christopher Loeb in a rage after the handcuffed burglary suspect called him a “pervert” over the stolen bag’s racy ­contents.

Then, court papers allege, the disgraced lawman forced lower-level cops to get their “stories straight” and keep him in the clear — intimidating them so badly that one even lied under oath on the witness stand.

Loeb was arrested on Dec. 14, 2012, at his mother’s Smithtown home, where authorities found “a cache of property stolen from numerous vehicles,” including from Burke’s police-issued SUV.

“The items stolen from Burke’s vehicle included his gun belt, magazines of ammunition, a box of cigars, a humidor and a canvas bag that contained, among other items, sex toys and adult pornography,” the fed documents say.

When Burke learned of the bust, he was so concerned about concealing the bag of smut that he raced over to the Smithtown house and tampered with the crime scene, the feds allege, grabbing the duffel and other belongings “in direct violation of police procedure and protocol.”

He then headed to the police station where Loeb was “handcuffed, hunched over and manacled to the floor” and proceeded to attack him, the feds say.

“Burke shook Loeb’s head violently, punched him in the head and body and attempted to knee Loeb,” court papers ­allege.

Knowing that Loeb was a heroin addict, Burke also allegedly threatened to kill him with a “hot shot” overdose of drugs laced with poison.

Although Loeb was unable to fight back, he called the chief a “pervert,” mentioning one piece of porn that Loeb mistakenly thought featured a minor on its cover.

“Burke then went out of control, screaming and cursing at Loeb and assaulting him until a detective finally said, ‘Boss, that’s enough, that’s enough,’ ” court papers allege.

Afterward, Burke allegedly bragged about the beating to other cops, including at a “department event” where he ­“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 also allegedly “referred to detectives who were present . . . as his ‘palace guards.’ ”

At a news conference announcing Burke’s arrest, US Attorney Robert Capers said, “No one is above the law.”

Burke, who faces up to 25 years in prison, pleaded not guilty at his arraignment in Central Islip federal court.