Thomas Spota, right, and his attorney Alan Vinegrad leave federal court in Central Islip on Oct. 25. AP Photo/Seth Wenig.

Suffolk County District Attorney Thomas Spota, who was charged more than three weeks ago with allegedly covering up a former police chief’s assault of an incarcerated suspect, says he will resign on Friday, according to his office.

But Christopher McPartland, Spota’s anti-corruption prosecutor and his co-defendant in the federal case, will remain with the office and was “reassigned to administrative duties unrelated to his former supervisory role,” said Robert Clifford, a spokesman for Spota’s office.

On Oct. 25, Spota and McPartland were indicted on charges of obstruction of justice, conspiracy to tamper with a witness, witness tampering and obstruction of an official proceeding. They are accused of taking steps to silence co-conspirators and witnesses to a 2012 incident in which James Burke, who was then chief of the Suffolk County Police Department, and other officers assaulted a man who was being held for allegedly breaking into Burke’s car and stealing items.

The day after his indictment, Spota said that he would resign at the “earliest opportunity after the resolution of normal administrative matters relating to my retirement.”

Clifford referred to the Oct. 26 statement when asked why Spota remained on the job until more than three weeks later.

Clifford said Emily Constant, Spota’s chief assistant, will step in as acting DA after Spota resigns. On Tuesday, Suffolk County Police Chief Timothy Sini, a Democrat, was elected as the county’s next district attorney after running on a platform that included a pledge to clean up the beleaguered office.

Sini, who won with 62 percent of votes, told Newsday that his transition into the office may include investigations into possible ethical or criminal violations by current staffers.