Former Suffolk police chief James Burke was sentenced to 46 months in prison Wednesday for beating a man who stole a duffel bag from his police-issued vehicle and orchestrating an elaborate scheme to conceal the crime.

Burke acted “as a dictator” in a cover-up conspiracy that “affected a whole police department,” U.S. District Judge Leonard Wexler said in imposing the sentence.

“He corrupted a system, not on one act, but for three years,” Wexler said.

Addressing the judge in federal court in Central Islip, Burke called his actions “a calamitous misdeed” and apologized to the victim, Christopher Loeb, the police department and his own family, “particularly my mother.”

Loeb, who is serving time for a parole violation, locked eyes with Burke in the courtroom while making his victim impact statement.

“I thought you were untouchable,” the Smithtown man told Burke. “Now look at us both, we are both incarcerated. The difference, besides the fact that my sentence is about to end and yours is only beginning, is that my actions reflected only me. ... Your crimes revealed deep problems in the entire Suffolk County law enforcement community.”

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The case started in December 2012, when Loeb, then 26, broke into Burke’s departmental sport utility vehicle and stole the duffel bag, finding a gun-belt, magazines of ammunition, a box of cigars, sex toys and pornography, prosecutors said.

Federal prosecutors said in a pre-sentencing memorandum that Burke’s obstruction scheme included “the recruiting of high-ranking officials from other county agencies to assist him in the obstruction and to give teeth to his threats.”

“SCPD members who witnessed the assault came under direct and extreme pressure from the defendants and others to conceal it,” prosecutors said.

Burke, 52, of St. James, faced 41 to 51 months in prison under the terms of a plea deal.

He pleaded guilty in February to obstruction of justice and violating the victim’s civil rights after a probe by special investigators reporting directly to Eastern District U.S. Attorney Robert Capers and FBI agents.

The 11 months Burke has spent in a federal detention center since his December arrest will be subtracted from his sentence. In addition, federal prisoners can get up to 15 percent off for good behavior. That means Burke could be out in 28 months.

Burke, formerly Suffolk’s highest-ranking uniformed officer, served as chief of department from January 2012 until his resignation in November 2015.

He appeared in court Wednesday in tan prison clothes and without his signature mustache.

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Burke apologized both to “the citizens of Suffolk County” and “the men and women of the Suffolk County Police Department.”

“It is my sincere desire that with this sentencing the focus can be on the great deeds and heroic actions that they perform every day and on every tour of duty,” he said.

Burke had sought to avoid time behind bars in order to care for his mother, who is seriously ill with cancer — an appeal for leniency that Loeb attacked.

“If you had been thinking about your mother when you had me chained to the floor, maybe you would not have had your officers threaten to rape mine, maybe you would not have assaulted me, and then maybe none of us would be in this courtroom today,” he said.

“I am not perfect,” he added, “ ... but the punishment for someone accused of petty thefts should never entail a vicious beating by the chief of police. ... What you did shook the foundation of an entire police department and the district attorney’s office, who I believe helped you get away with crimes, at least for a short period of time.”

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Burke was a longtime protégé of Suffolk District Attorney Thomas Spota. Before he was named chief, Burke headed Spota’s detective unit.

Newsday reported in June that federal investigators are probing whether Spota and one of his chief assistants, Christopher McPartland, took part in the cover up of the assault on Loeb.

Spota has said he did nothing wrong in the Loeb case, and McPartland and his attorney have declined to comment.

A spokesman for the district’s attorney’s office did not return phone calls seeking comment Wednesday. Spota also could not be reached.

In addition to the 46-month sentence, Burke was sentenced to three years of supervised release.

“My client is going to do his time like a man, and he’s going to come out and be a productive member of society,” said Burke’s attorney, John Meringolo, of Manhattan, after the sentencing.

Meringolo had asked the judge not to impose any jail sentence, citing the illness of Burke’s mother, Frances, whom Burke cares for, and for what he has said is his client’s otherwise “extraordinary career history.”

Prosecutors Lara Treinis Gatz and John Durham urged the judge to sentence Burke to the maximum — 51 months.

“Isn’t conduct the best proof of character? Not how a person acts on his best day, but how a person acts on his worst day,” Treinis Gatz said in court. “On Mr. Burke’s worst day ... he hurt Mr. Loeb and the law enforcement community as whole, irrevocably.”

Eastern District U.S. Attorney Robert Capers was among those who attended the sentencing in a courtroom that was packed to overflowing, as was an adjoining courtroom to which the proceedings were piped into.

In a statement, Capers said Burke “considered himself untouchable. He abused his authority by brazenly assaulting a handcuffed prisoner, he pressured subordinates to lie to cover up his criminal acts, and he attempted to thwart the civil rights investigation into his conduct.”

Capers said the sentence delivered a message that “no one is above the law, and that the consequences for such egregious behavior are severe.”

Suffolk Police Commissioner Timothy Sini stressed afterward that the Burke case is not a reflection of the department as a whole these days. “I have often been humbled by the professionalism and bravery of our officers,” Sini said.

More than 80 people wrote letters to the judge asking for leniency, saying the former chief’s entire career should be taken into account.

Wexler said he read the letters but wasn’t swayed.

“I feel Mr. Burke was acting as a dictator,” he said. “How do dictators operate? If you are good to them, they are good to you, all these people — and I believe them, I believe every letter that was sent on his behalf. He did something good for them. But he also did bad if you were not on his side.

“That’s corruption.”