A federal grand jury indicted James Burke, the former Suffolk County Police chief of department, Tuesday, several sources said.

The grand jury had been investigating allegations that Burke and other police officers beat and then covered up the assault on a Smithtown man who stole a duffel bag from the chief’s department SUV.

Burke, of St. James, the highest-ranking uniformed officer on the force until he resigned in October, was scheduled to be arraigned Wednesday at the federal court in Central Islip, the sources said.

Top Justice Department officials in the area are scheduled to hold a news conference on the case Wednesday.

Burke’s attorney, Joseph Conway, of Mineola, said Tuesday night that he has not been contacted about surrendering his client. The Eastern District could not be reached for comment.

The exact charges Burke faces could not be determined immediately, but the grand jury was known to be questioning witnesses about the possibility that violations of civil rights occurred, as well as a subsequent cover-up of the attack, which would amount to obstruction of justice.

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More than a dozen Suffolk police officers in 2012 were either at the Smithtown precinct or at the home of Christopher Loeb at the time the Smithtown man was detained. Loeb has said he was assaulted initially at his home by officers and subsequently at the precinct, where he was beaten by Burke and other officers.

None of those officers are believed to have been charged so far in the case, and several are believed to have been cooperating with federal investigators.

The grand jury at the federal courthouse in Central Islip started in late spring to look into the case. The new grand jury had revived an investigation that had remained dormant since the beginning of 2014.

Both grand jury investigations were triggered by the 2012 theft of Burke’s duffel bag. Newsday had reported the existence of the new grand jury probe last month.

Since those same questions were asked during the initial investigation without any charges being brought, it is believed that federal investigators have acquired new evidence, the sources said.

That evidence might include wiretapped information, several of the law enforcement officers involved changing their accounts of what occurred or both, the sources said.

Several of the sources have said that some officers are now cooperating with investigators.

At least three officers have been identified by sources as cooperating with the grand jury. Their attorneys have declined to comment.

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Federal investigators have focused their questioning of the Suffolk police almost solely on two different subjects: what happened at Loeb’s house and the precinct, and what was in Burke’s duffel bag, the sources said.

The duffel bag question centered on if it contained pornography, the sources said.

Suffolk police have said the duffel contained a department gun belt, ammunition, handcuffs, a whistle and a box of cigars.

Amy Marion, an attorney for Loeb, 29, has said that her client claims the duffel contained sex toys and DVDs of “nasty porn.” Marion, of Garden City, said Burke’s reason for going to the scene was to recover the duffel and that was the motivation for his being enraged enough to later beat her client in the precinct.

Loeb pleaded guilty to the 2012 theft of the duffel bag from a department SUV parked in front of then-Chief Burke’s St. James home.

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Loeb also has filed a federal lawsuit against the county, Burke and other police officers, accusing them of violating his civil rights.