A federal judge Wednesday set ex-Suffolk Police Chief James Burke’s trial date for March 21 on charges he beat a prisoner who had stolen a duffel bag from his department SUV and masterminded a cover-up.

Burke, the former top uniformed cop in the county, appeared Wednesday in Central Islip federal court wearing federal jail khakis and without his mustache.

He calmly answered routine questions from U.S. District Judge Leonard Wexler in a clear voice, his right leg shaking throughout much of the brief proceeding.

Burke pleaded not guilty and remains held without bail.

Asked how his client is holding up in jail, Conway said after the hearing, “It’s not easy, but he’s adapting.”

An indictment unsealed Dec. 9, the day federal agents arrested Burke in the driveway of his St. James home, accuses him of beating a handcuffed prisoner, Chistopher Loeb, and enlisting unnamed officers and others in a massive cover-up of the alleged assault.

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Suffolk officers had arrested Loeb earlier in the day on Dec. 14, 2012, after, they said, he stole a duffel bag from Burke’s unlocked SUV parked in front of the 29-year-department veteran’s home.

Since Burke’s arrest, prosecutors have handed over 3,000 pages of discovery to the defense, with more coming in the next two weeks, Eastern District Asst. U.S. Attorney Lara Treinis Gatz told Wexler Wednesday.

The judge set the next hearing date for Feb. 2.

Conway said the defense is concentrating on preparing for trial and not on appealing Burke’s detention because historically, it’s unlikely it would be overturned.

On Dec. 11, Burke was first ordered held without bail as a danger to the community, after federal prosecutors said he still maintained considerable influence over the department. They had argued that several police union officials and others in the department, though never charged, were engaged in the alleged cover-up and continued to support Burke even while he was under investigation. No co-conspirators were named in court papers.

Further, the prosecutors argued that fear of Burke still pervaded parts of the department.

The ex-chief’s attorneys, Conway and Nancy Bartling of Mineola, disagreed with the prosecutors’ arguments, saying that since Burke was no longer police chief, he would have no access to anyone in the department, including potential witnesses called to testify at his trial.

Wexler concurred with Gatz and fellow Eastern District federal prosecutor James Miskiewicz.

“I find the corruption of an entire department by this defendant is shocking,” Wexler said at Burke’s bail hearing.

Burke faces charges — depriving a person of civil rights and a conspiracy to obstruct justice — that usually call for a sentence of 5 to 5½ years under federal sentencing guidelines. But, if convicted, and depending on particular individual circumstances, a judge could sentence Burke to up to 20 years.