James Burke, Ex-Suffolk County Police Chief

CENTRAL ISLIP, N.Y. — The former police chief of Suffolk County pleaded guilty on Friday to federal charges stemming from accusations that he beat a suspect in custody, threatened to kill him and then coerced his fellow officers into covering up the misconduct.

The former chief, James Burke, 51, who was known for his swaggering confidence as the leader of one of the region’s largest police departments, was subdued in Federal District Court here as the charges against him were read aloud.

“I plead guilty, Your Honor,” said Mr. Burke, wearing a drab khaki prison uniform.

Since the federal inquiry into Mr. Burke’s actions began some three years ago, investigators have expanded their inquiries and are now examining the workings of the Police Department and the district attorney’s office.

Robert L. Capers, the United States attorney for the Eastern District of New York, said the investigation was continuing and would seek out those who might have been involved in wrongdoing.

“The defendant violated his oath and responsibilities as a law enforcement officer by exacting personal vengeance, assaulting a handcuffed suspect and abusing his authority as the highest ranking uniformed member of the Suffolk County Police Department,” Mr. Capers said in a statement. “Despite the efforts of the defendant and his co-conspirators to obstruct the federal investigation, he has been brought to justice.”

Joseph Conway, Mr. Burke’s lawyer, later told reporters that he planned to argue for a sentence of less than five years in prison for violating the suspect’s civil rights and conspiring to obstruct justice. The maximum possible sentence for the civil rights charge is 10 years in prison; for the obstruction charge, it is 20 years.

“He realized what he did here, and he wants to own up to it,” Mr. Conway said. “He’s very remorseful.”

He was brought to a precinct house and shackled to the floor.

In a 2013 court hearing, Mr. Loeb testified that when he asked for a lawyer, one detective told him, “This isn’t ‘Law & Order’; you’re not going to get an attorney.”

When Mr. Burke entered the interrogation room, Mr. Loeb “was handcuffed and chained to an eyebolt fastened to the floor,” according to prosecutors.

“Chief Burke grabbed me by my cheeks and hit me on the top of my head,” Mr. Loeb testified during his 2013 trial, during which he was found guilty and sentenced to three years in prison.

Mr. Loeb responded to the thrashing by calling Mr. Burke “a pervert” and mocking him for the pornography he found in his car, according to federal prosecutors.

At that point, prosecutors said, Mr. Burke “went out of control, screaming and cursing at Loeb and assaulting him until a detective finally said, ‘Boss, that’s enough, that’s enough.’”

After the interrogation, Mr. Burke pressured the detectives who witnessed the assault to conceal it.

“Those efforts continued even after the F.B.I. and the U.S. attorney’s office opened an investigation of the assault in May 2013,” according to a statement released by prosecutors announcing Mr. Burke’s indictment in December.

After Mr. Burke was arrested, Judge Leonard Wexler took the unusual step of denying him bail, saying he posed a danger to the community.

“I find the corruption of an entire department by this defendant is shocking,” Judge Wexler said in December.

Investigators are looking into the conduct of two of Mr. Spota’s protégés — Mr. Burke and the district attorney’s top anticorruption prosecutor — and any role they may have had in what federal prosecutors have described as a conspiracy to obstruct justice, three officials familiar with the investigation told The New York Times earlier this year.

The new Suffolk police commissioner, Tim Sini, is a former assistant United States attorney from the Southern District of New York, and he has hired a former federal corruption investigator, John Barry, to review the department’s internal affairs files.

At a court hearing after Mr. Burke’s arrest, a federal prosecutor, James Miskiewicz, described a pattern of abuse, including the use of a contractor for the district attorney’s office to install a GPS device on a deputy police commissioner’s car.

Mr. Burke was hoping to “to dig up blackmail dirt on her,” Mr. Miskiewicz testified, calling the episode “something out of the K.G.B.”

Mr. Spota and Mr. Burke have been close for decades, and the district attorney helped Mr. Burke secure his job as the top officer for much of Long Island, despite a sometimes checkered history.

Two decades ago, as a sergeant, Mr. Burke had a sexual relationship with a prostitute, according to an internal affairs investigation that accused Mr. Burke of accidentally leaving his handgun with the woman, Newsday reported.

Mr. Burke not only survived that incident but also thrived. He was named chief in 2012, the highest-ranking uniformed position in the department, which, like New York City’s, is led by a civilian commissioner.

Compared with those in other departments, officers in the Suffolk agency are well paid, making $125,000 in base pay. That is about $50,000 more than their counterparts in New York City, and it does not include overtime pay, which can be substantial, or the extra money officers receive for each year on the job.

Detectives and sergeants have been known to earn more than $200,000 a year. The police unions on Long Island are so wealthy they have formed a “super PAC” to flood local elections with campaign donations.