CENTRAL ISLIP, N.Y. (CBSNewYork) — Longtime Suffolk County District Attorney Thomas Spota and one of his top aides were indicted by a federal grand jury Wednesday, on charges of obstructing a federal civil rights investigation into the beating of a handcuffed prisoner by the county’s former police chief.

Charges against Spota and Christopher McPartland, the DA’s chief of investigations and the office’s government corruption bureau, include witness tampering and obstruction of justice.

As CBS2’s Jennifer McLogan reported, Spota is the longest-serving district attorney in Suffolk County history. He announced in May that he was not planning to run for a fifth term in November, and some wondered if we might now know why.

It was a stunning fall from grace for Spota, a Democrat who was elected 16 years ago as a corruption fighter.

The charges stem from the alleged cover up of ex-Suffolk County police Chief James Burke’s beating of a suspect in 2012.

The district attorney faces charges of conspiracy to tamper with witnesses, obstructing an official proceeding, and obstruction of justice.

“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,” stated Acting United States Attorney Bridget Rohde. “Abuses of power by law enforcement authorities cannot and will not be tolerated. There are serious consequences to such actions.”

“While FBI agents were working to restore justice in a civil rights investigation, District Attorney Thomas Spota and Assistant District Attorney Christopher McPartland were conspiring to obstruct it, as alleged today,” stated FBI Assistant Director-in-Charge William Sweeney. “The crimes they’re charged with are rivaled only by the conduct they allegedly attempted to conceal. Make no mistake about it, this type of activity will not be tolerated. Today our message is clear: those seated at the highest levels of the law must still operate within its confines – there are no exceptions.”

But defense attorney Alan Vinegrad said: “Tom Spota committed no crime. In fact, for many years of a long and distinguished career, Tom has worked hard to investigate and prosecute crime, and deliver justice to the residents of Suffolk County. Tom categorically denies the government’s charges, and he looks forward to vindicating himself in court.”

Former police Chief Burke is currently serving a prison sentence of three years and 10 months after pleading guilty to assaulting a handcuffed man who had broken into his sport-utility vehicle and taken his gun belt, ammunition, a box of cigars and a bag containing sex toys and pornography. Prosecutors said Burke then lied and asked others to lie on his behalf to cover up the beating.

The man who was beaten, Christopher Loeb, spoke Wednesday.

“Every time I asked for a lawyer, I got hit again. I got hit again. I got choked. I got choked. I got punched. I got slapped. I got kicked,” Loeb said.

According to the federal indictment, Spota and McPartland had meetings and conversations with Burke and other police officers in which they “agreed to conceal Burke’s role in the assault and to obstruct and attempt to obstruct the federal investigation in order to protect Burke.”

Prosecutors said Spota and McPartland used “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” from federal investigators.

Spota looked weary and pale before a judge at U.S. District Court in Central Islip as he pleaded not guilty. He put his home up as collateral for the $500,000 bond and surrendered his passport.

The timing of the arrest – so near an upcoming election – is making waves. Suffolk County police Commissioner Timothy Sini hopes to succeed Spota.

“I was asked to become police commissioner to clean up Burke’s mess,” Sini said. “I’m now going to become district attorney and clean up Spota’s mess.”

Sini said he would clean house when he takes office if elected DA.

“Obviously, a lot of movement; a lot of changes are going to occur,” he said.

Suffolk County Legislator Robert Trotta (R-13th) added: “Welcome to the cesspool that I call Suffolk County. When we have this going on in our county, it is an embarrassment, and believe me, this is the tip of the iceberg.”

Calls for Spota to resign went unanswered.