Longtime Suffolk County District Attorney Tom Spota and his top aide pleaded not guilty Wednesday to four federal charges, including witness tampering and obstruction, in an indictment related to the now disgraced police chief James Burke.

According to the unsealed indictment, Spota and also indicted top aide Christopher McPartland had "numerous" meetings and phone conversations about the assault on burglary suspect Christopher Loeb, as well as the allegations against Burke.

In 2012, Burke assaulted Loeb – who had allegedly stolen Burke's gym bag from his SUV. The bag contained the former chief's gun belt, sex toys and pornography. 

Burke drove to Loeb's house to retrieve the bag after he was identified as the suspect. Burke then allegedly "punched and kicked Loeb in the head and body" after Loeb was taken to a nearby precinct. Prosecutors had said Burke, "together with other members" of the Suffolk County Police Department, tried to cover up the assault.

The Department of Justice began investigating Burke and Spota's office shortly after the 2012 incident. Prosecutors say Spota and McPartland agreed to conceal Burke's role in the assault. They are accused of intimidating and threatening a number of witnesses.

Burke and Spota have a 30-year history that began when Burke was a teenage witness in the John Pius murder trial. Spota was an assistant district attorney on the case.

Spota was asked several times by News 12 Long Island Wednesday afternoon if he plans to resign. He did not answer.

Both Spota and McPartland put up $500,000 bond packages. They are due back in court on Dec. 1.

Burke was sentenced last November to 46 months in prison after making a guilty plea.