By Rashed Mian, Christopher Twarowski & Spencer Rumsey

Former Suffolk County Police Chief of Department James Burke was arrested Wednesday morning by federal authorities for covering up a retaliatory assault on a suspect and misleading federal agents investigating the case.

Federal authorities unsealed a two-count indictment charging Burke with violating the suspect’s civil rights and conspiracy to obstruct justice.

Burke, who retired in October amid reports of a federal investigation, was handcuffed at his St. James home Wednesday morning and taken to the FBI’s Long Island field office in Melville for processing. Silent during his arraignment before US District Court Judge Leonard Wexler in Federal Court in Central Islip Wednesday afternoon, Burke will be held in protective custody until a bail hearing Friday, which was sealed upon his attorney’s request.

Robert Capers, US attorney for the Eastern District of New York, at a press conference in Central Islip announcing the indictment, said, “No one is above the law.”

Diego Rodriguez, FBI assistant director-in-charge of the New York field office, told reporters, “When an officer’s actions threaten to obstruct the integrity of an investigation, they unjustly call into question the reputation of those among them.”

The case against Burke centers around the December 2012 arrest of Christopher Loeb of Smithtown. Loeb was suspected of breaking into several vehicles in Suffolk, including Burke’s department-issued SUV, which contained a duffel bag of personal items, including Burke’s gun belt, ammunition, a box of cigars, a humidor, clothes, toiletries, and other items, authorities said.

Several members of the Suffolk Police and the New York State Probation Department arrested Loeb inside his mother’s Smithtown home. Burke then went to Loeb’s house to retrieve the duffel bag, Capers said. Capers noted that it’s “unusual” for a high-ranking officer to respond to a crime scene and later confront a suspect who had victimized him.

“That was an unusual occurrence,” Capers told reporters.

Afterward, Burke, the highest-ranking uniformed officer in the department, traveled to Suffolk police’s 4th Precinct, where Loeb was handcuffed and chained to an eye bolt fastened to the door, authorities said.

Burke allegedly entered the interrogation room with other officers and “slapped and punched” Loeb in the head and body, according to the federal indictment. Loeb confessed to the robberies, authorities said.

A cover-up ensued, the indictment alleges.

Loeb has been outspoken about what occurred after his arrest, and he’s accused Burke of assault. He has since filed a federal lawsuit against the police department.

After Loeb’s arrest Burke and other members of the police department met “on multiple occasions to discuss” Loeb’s assault allegations “and agreed to conceal Burke’s role in the assault,” according to the indictment.

Capers said the meetings were held in an effort to “agree on ways to get their story straight.” It was at one of the meetings that they agreed to “provide false information and to withhold relevant information from the FBI,” the indictment alleges.

Burke went as far as pressuring a Suffolk police detective to lie under oath and testify that it never happened, authorities said.

The FBI first opened an investigation into the alleged assault in April 2013. In June the agency subpoenaed members of the police force.

Capers said the investigation is ongoing. He did not say if the detective who lied under oath is under investigation. He also declined to elaborate about the “other items” that were inside Burke’s duffel bag. Loeb has suggested that there was pornographic material in the bag. The items were personal, Capers said, and possession of such items are not illegal.

Loeb was sentenced in April last year to three years in prison for the duffel bag theft after pleading guilty to criminal possession of a weapon. At the time, authorities said the bag contained Burke’s gun belt and ammunition.

Burke retired in October after the FBI had reopened the case against him. Outgoing Suffolk County Police Commissioner Ed Webber praised Burke following the announcement, saying Burke “is one of the most outstanding supervisors, investigators, and trainers in the history” of the department. In November Webber announced he’s retiring as of Jan. 25, 2016.

Burke, whose father and grandfather were both New York City cops, was 14 years old when he was a witness in the murder case of John Pius, Jr., a 13-year-old Smithtown teen whom classmates suffocated with rocks in 1979 for stealing a dirt bike. Three were convicted; a fourth classmate’s conviction was later overturned. Burke spent a year as a New York City police officer in 1985, and joined the Suffolk County Police in 1986 at 21, first as a patrolman in North Amityville and later as an undercover narcotics officer.

He later spent a decade as chief investigator under Suffolk County District Attorney Thomas Spota, the former chief prosecutor in the Pius case.

The Loeb incident is not the first time the 30-year veteran of the Suffolk County Police Department has come under scrutiny.

Burke was the subject of a 1995 Internal Affairs investigation that concluded allegations he “engaged in a personal, sexual relationship” with “a convicted felon known to be actively engaged in criminal conduct including the possession and sale of illegal drugs, prostitution and larceny,” “engaged in sexual acts in police vehicles while on duty and in uniform,” and “failed to safeguard his service weapon and other departmental property” were “substantiated,” according to its report.

Burke also came under fire in 2012 for the controversial disbandment of a highly successful Suffolk County Police Department component of the FBI’s joint Long Island Gang Task Force—its dismantling was the subject of a Press cover story “Turf War: Is SCPD Playing Politics By Leaving FBI’s LI Gang Task Force?

Yet instead of discipline, Burke received promotions, moving up through SCPD’s ranks throughout the years to the top position. Spota, along with County Executive Steve Bellone—who appointed Burke police chief in 2012—facilitated his meteoric ascent.

Burke’s indictment was reverberating throughout Suffolk County government Wednesday morning, with county lawmakers still expressing surprise regarding Burke’s unceremonious departure two months earlier, and shock and dismay about his latest fall from grace.

“This whole situation is upsetting to me,” lamented Legis. Leslie Kennedy (R-Smithtown). “We will find out what is truthful and what is not during the course of the process.”

Suffolk District Attorney Thomas Spota did not return a call for comment. Both Suffolk County Executive Steve Bellone and Police Commissioner Webber declined to comment, citing the ongoing investigation.

[Photo: Disgraced former Suffolk County Police Chief James Burke was arrested by federal agents Wednesday, Dec. 9, 2015 and indicted on civil rights violations and conspiracy charges. (Long Island Press)]

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