Hughes, 40, of Tupelo appeared before Magistrate Judge S. Allan Alexander, who set his bond at $10,000.
His travel also was restricted to north Mississippi.
Alexander set a trial date for Dec. 17 in Oxford before Chief Judge Michael P. Mills.
Hughes was charged with the civil rights violations Oct. 12 and his sealed indictment was posted Oct. 31 along with the court proceedings, although the indictment was dated Oct. 25.
He is represented by attorneys Anthony Farese of Ashland and Jason Herring of Tupelo.
Hughes was a decorated trooper with the Mississippi Highway Patrol until recently. MHP officials decline to give any details about his termination, although they say the Lee County jail incident was turned over to the FBI to investigate.
If convicted, he faces up to 10 years in prison.
The initial federal charges against Hughes were dated two days before the five-year statute of limitations ran out.