District Attorney Thomas Spota, 76, and Christopher McPartland, 51, the head of the district attorney's political corruption unit, were taken into custody by the FBI Wednesday.
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They are both charged with taking part in the cover-up of former Suffolk Police Chief James Burke's assault of a suspect, Christopher Loeb, in 2012.
They're facing charges of tampering with witnesses, witness tampering, obstruction of justice and deprivation of civil rights.
Spota entered a plea of not guilty during an afternoon court appearance. His bail was set at $500,000.
"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," Acting United States Attorney Bridget Rohde said. "Abuses of power by law enforcement authorities cannot and will not be tolerated.
There are serious consequences to such actions."
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Burke is serving a 46-month federal sentence for violating Loeb's civil rights in 2012.
Before Burke was sentenced in February 2016, federal prosecutors claimed in court documents that there was -- "the recruiting of high-ranking officials from other county agencies to assist him in the obstruction and give teeth to his threats. SCPD members who witnessed the assault came under direct and extreme pressure from the defendant and others to conceal it."
Spota announced earlier this year that he would not run for a fifth term in November. He is the longest-serving district attorney in county history.