Yury Nagornykh was named as a key player in an investigation into state-sponsored doping by the World Anti-Doping Agency (WADA) published weeks before the 2016 games.
The report said Nagornykh was routinely informed about positive doping tests and decided "who would benefit from a cover-up and who would not".
The Russian government website made no mention of the doping scandal, saying that Nagornykh had asked to resign and his dismissal had been signed by Prime Minister Dmitry Medvedev.
Nagornykh's departure follows that of his former boss, sports minister Vitaly Mutko, who was given the post of deputy prime minister overseeing sports last week, and the head of Russia's Olympic Committee.
(Reporting by Maria Tsvetkova; Editing by Robin Pomeroy)
