CENTRAL ISLIP, N.Y. — A district attorney on eastern Long Island and a top aide were charged Wednesday with intimidating witnesses in a federal civil rights investigation into the beating of a handcuffed prisoner by a police chief.

Democratic Suffolk County District Attorney Thomas Spota and the chief of his anti-corruption bureau, Christopher McPartland, were named in an indictment charging them with obstruction of justice, witness tampering and other offenses related to the case against former county Police Chief James Burke.

Both pleaded not guilty at their arraignment in federal court on Long Island.

“While FBI agents were working to restore justice in a civil rights investigation, (the defendants) were conspiring to obstruct it, as alleged today,” said William Sweeney, head of the FBI’s New York Office. “The crimes they’re charged with are rivaled only by the conduct they allegedly attempted to conceal.”

Both men were released on $500,000 bond, and a judge restricted their travel to the continental United States.

“Tom categorically denies the government’s charges, and he looks forward to vindicating himself in court,” Spota’s attorney, Alan Vinegrad, said outside the courthouse with Spota, who didn’t speak and ignored shouts from reporters asking him if he was going to resign.

Suffolk County Executive Steve Bellone and Police Commissioner Timothy Sini, both Democrats, have called for the prosecutor to resign. Sini is running for district attorney in November.

Spota, 76, is not seeking re-election after 16 years in office.

In a statement, McPartland’s lawyer said his client vehemently denies the charges.

“Chris McPartland has always been an honest and dedicated public servant,” Larry Krantz said.

As part of the bail conditions, Spota and McPartland, 51, are forbidden from speaking with each other at work unless a third person is present.

Last year, Burke was sentenced to nearly four years in prison for orchestrating a department cover-up after beating a handcuffed man for stealing embarrassing items from his department-issued SUV. Burke was a longtime protege of Spota’s and once worked as an investigator in the district attorney’s office before being named chief of the Suffolk County Police Department, one of the largest suburban departments in the country with 2,500 officers.

As a child, Burke was the key witness in a murder trial of a young boy in a case prosecuted by Spota, who was then an assistant district attorney.

In a pre-sentencing letter, prosecutors said “high-ranking officials” from other county agencies helped Burke silence potential whistleblowers after he pummeled a heroin addict who had taken his gun belt, ammunition, a box of cigars and a bag containing sex toys and pornography.

Officers subpoenaed by FBI agents investigating the 2012 beating were interrogated afterward about whether they had talked, prosecutors said. Unnamed co-conspirators had warned some that if they admitted wrongdoing, their union would not pay their legal fees, prosecutors said.

According to the indictment, Spota, McPartland, Burke and other police officers had numerous meetings and telephone conversations discussing the assault of “John Doe” and how to conceal Burke’s role in the assault.

The defendants used their authority “to obstruct and attempt to obstruct the federal investigation by, among other means, using intimidation, threats and corrupt persuasion to pressure multiple witnesses, including co-conspirators, not to cooperate with the federal investigation, to provide false information, including false testimony under oath, and to withhold relevant information to prosecutors,” the court paper said.