WASHINGTON — Since 1997, Harold Nicholson has been locked in a federal prison in Oregon, the highest-ranking officer of the Central Intelligence Agency ever convicted of espionage.

But even as federal inmate No. 49535-083, Mr. Nicholson never really retired as a Russian spy, federal prosecutors say. In an indictment unsealed Thursday, Mr. Nicholson and his 24-year-old son, Nathan, were charged with using jailhouse visits, coded letters and clandestine overseas meetings to sell more secrets to the Russians over the last three years, in a scheme Mr. Nicholson hatched from his prison cell.

The Nicholsons pleaded not guilty on Thursday in federal court in Portland, Ore., and the public defender’s office was appointed to represent them.