Ponomaryov told the Russian Regnum news agency in 2006 that the Federal Prison Service chief, Yury Kalinin, was "the author of a sadistic system of torture."
The country's Kremlin-nominated human rights commissioner, Vladimir Lukin, also described prison conditions in many Russian facilities as "close to torture" in a recent interview.
Ponomaryov said prosecutors falsely charged him with accusing Kalinin of a serious crime, The Moscow Times said Tuesday. Slander carries a maximum three-year prison term.
Outgoing Russian President Vladimir Putin signed a law in 2006 designating the slander of public officials as a form of extremism.
Ponomaryov served in the State Duma and is the director of the For Human Rights group.