Vladimir Popovkin has headed the Roscosmos space agency since April 2011.
Deputy Prime Minister Dmitry Rogozin, who oversees the defense industry, said the reprimand was unrelated to a recent failure of a rocket launch, RIA Novosti reported.
On July 2, a Proton-M rocket carrying three Glonass navigation satellites exploded shortly after launch from the Baikonur space center in Kazakhstan.
"Vladimir Popovkin has been reprimanded. ... But this reprimand has nothing to do with the recent Proton-M accident," Rogozin tweeted Friday.
In July, Russia's Audit Chamber issued a report saying the Federal Space Program was ineffective and blighted by poor management and use of funds for space projects.
Russia's space program has been hampered by a number of failures in recent years, most of them blamed on faulty hardware.
The Audit Chamber criticized Roscosmos for launching only 47 percent of Russia's required number of satellites into orbit from 2010 to 2012.