Members of the Suffolk police department who helped former chief James Burke cover up his beating of a heroin-addicted thief have been indicted and pleaded guilty in secret proceedings in federal court, according to a motion filed Wednesday in state Supreme Court.

The motion, filed in Riverhead on behalf of the man Burke beat, Christopher Loeb, 30, of Smithtown, seeks to set aside Loeb’s guilty plea to criminal possession of a weapon after a pretrial hearing in 2013. Loeb was sentenced to 3 years in prison in 2014.

“Criminal prosecutions should not be built on egregious police misconduct and perjury,” said Loeb’s attorney, Bruce Barket of Garden City. “It decimates the integrity of the system.”

Barket said attorneys involved in the case have told him at least six officers and detectives have pleaded guilty to crimes. Burke pleaded guilty in February to beating Loeb on Dec. 14, 2012, and orchestrating a cover-up, and is serving a prison sentence of 46 months.

“No one currently employed by the Suffolk County Police Department has pled guilty to any crimes in connection with Christopher Loeb,” said Assistant Police Commissioner Justin Meyers. Several officers and detectives associated with the Loeb case have since retired. Meyers would not say if others have retired or been fired. He added that when Commissioner Timothy Sini took office earlier this year, he “took aggressive steps to ensure the integrity of the department.”

Beyond that, Meyers said, “Our partners at the U.S. Attorney’s office have asked us not to comment and we are going to honor their request.”

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A spokesman for the U.S. attorney’s office for the Eastern District declined to comment on Barket’s claim.

Sources familiar with the case confirmed law enforcement officers were indicted, but would not say how many.

In one of the indictments a Suffolk officer was charged with conspiracy to commit obstruction of justice, and agreed to cooperate with authorities as part of a plea deal, sources said. That officer has not been sentenced.

In another case, an officer who had “significant information” to provide against Burke but was deemed to be less culpable was granted immunity, according to the sources.

Loeb testified at the pretrial hearing that he had stolen a duffel bag from Burke’s police-issued sport utility vehicle, and said that in addition to a gun belt, it contained “disgusting pornography,” sex toys and other items. Burke personally retrieved the duffel bag before it could be kept as evidence.

During the hearing before state Supreme Court Justice Martin Efman, officers and detectives denied searching Loeb’s house on Burke’s orders and said they did so only to assist probation officers who were arresting Loeb for having brass knuckles.

Officers and detectives also testified they saw Burke take a look at Loeb at the Fourth Precinct in Hauppauge, but denied witnessing or participating in a beating. Efman found the officers to be credible, but Barket said Burke’s guilty plea showed they were all lying.

The witnesses at the pretrial hearing included Det. Thomas Cottingham, Det. Anthony Leto, Det. Christopher Nealis, Det. Kenneth Regensburg, Det. Keith Sinclair, Sgt. Michael Kelly and Officer Brian Draiss. Witnesses said Det. Kenneth Bombace was involved in the case, too.

Since Burke’s plea, Loeb’s new motion says that “numerous other members of the Suffolk County Police Department have been indicted, and have pled guilty to crimes committed against Loeb in connection with this incident, including others who testified at Loeb’s suppression hearing. Their identities have not yet been disclosed, and their files are currently sealed because the investigation is still ongoing.”

The motion does not reveal the source of that information. There were no other details on the cases.

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A special prosecutor, William Ferris of Islandia, will handle the motion because of Burke’s close ties to Suffolk District Attorney Thomas Spota, which date to when Burke was a teenage witness against four defendants in the notorious 1979 murder of 13-year-old John Pius. Ferris said he had just received Barket’s motion and needs time to consider the arguments.

His reply to Barket’s motion is due Jan. 6.

Burke’s Manhattan-based attorney, John Meringolo, said he was unaware of the filing and he declined to comment.

With Robert E. Kessler