Suffolk County District Attorney Thomas Spota, On Nov. 10, 2011, Suffolk County District Attorney Thomas Spota, center, leaves Suffolk County Court in Riverhead, New York. Federal authorities say Spota has been indicted in connection with a cover-up in a 2012 police assault case. (AP photo by John Dunn)

Suffolk County District Attorney Thomas Spota will resign, he announced Thursday, a day after federal prosecutors indicted him on charges of helping to cover up a police chief’s beating and threatening of a suspect.

“I will be leaving my post as district attorney at the earliest opportunity after the resolution of normal administrative matters relating to my retirement,” Spota said in a statement. “The governor will be notified of my decision today. The chief assistant district attorney, Emily Constant, will thereafter assume my duties and responsibilities.”

Spota, who took office in 2002 and who was re-elected three times, was the longest-serving DA in Suffolk County history. But in recent years, news reports had indicated that federal investigators had Spota and his anti-corruption assistant prosecutor, Christopher McPartland, in their sights.

On Wednesday, both Spota and McPartland were finally charged, as prosecutors from the U.S. Attorney’s Office for the Eastern District of New York unsealed an indictment in Central Islip. It charged both Spota and McPartland, the office’s chief of investigations and chief of the government corruption bureau, with witness tampering and obstruction of an official proceeding, and conspiracy to do the same. It said that a yearslong investigation had exposed efforts by the men to silence witnesses, including co-conspirators, who were set to describe how a former Suffolk County police chief badly beat a suspect detained after allegedly breaking into the chief’s car.

The suspect, an alleged heroin user named Christopher Loeb, also had been accused in 2012 of stealing from the car the chief’s duffel bag containing sex toys, pornographic DVDs and cigars.

By April 2013, federal authorities disclosed that they had initiated a grand jury investigation into Loeb’s beating. And early on, reports indicated that Spota and McPartland were included among county law enforcement officers being scrutinized.

Spota had met the police chief, James Burke, in the 1970s, when Burke was a teenager. And after being elected and entering the DA’s office in 2002, he had brought Burke, whom he considered a protege, into the office as a key investigator, news reports say.

Last year, Burke pleaded guilty to beating Loeb and was sentenced to 46 months in prison.

On Wednesday, Spota and McPartland were accused in the indictment of having used their positions to intimidate and pressure unnamed witnesses who’d been set to finger Burke in Loeb’s beating.

The six-page document said Spota and McPartland had pressured witnesses into lying to federal agents, and into giving false and incomplete testimony to grand jurors. But the indictment failed to detail how the alleged pressuring was done.

Spota, 76, entered a not guilty plea at the Central Islip federal courthouse on Wednesday. His lawyer, Covington & Burling partner Alan Vinegrad, claimed his client’s innocence outside the courthouse.

McPartland’s counsel, Krantz & Berman attorney Larry Krantz, also released a statement saying that his 51-year-old client was similarly innocent.

My client “vehemently denies the charges and asserts his innocence,” Krantz said. “He looks forward to his day in court.”

He added, “Chris McPartland has always been an honest and dedicated public servant.”

Acting U.S. Attorney Bridget Rohde for the Eastern District of New York said on Wednesday, “Prosecutors swear oaths to pursue justice and enforce the law. Instead of upholding their oaths, these defendants allegedly abused the power of the Suffolk County District Attorney’s Office, attempted to cover up the assault of an in-custody defendant, and attempted to thwart a federal grand jury investigation.”

Spota announced in May he would not seek re-election as district attorney.

In a bail letter to U.S. District Judge Leonard Wexler of the Eastern District of New York, the government on Wednesday asked for “significant” secured bonds and “stringent conditions” of pretrial release of Spota and McPartland.

“There is a serious risk that the defendants will continue to obstruct or attempt to obstruct justice, and continue to threaten, intimidate or attempt to threaten or intimidate prospective witnesses without these conditions,” the letter, signed by Assistant U.S. Attorney Lara Gatz, stated. Gatz is heading up the case for the government.

Wexler also oversaw Burke’s trial. The government filed a motion for related case designation with the Burke case.

Colby Hamilton contributed reporting.