Oleg Ostapenko, previously deputy defence minister, was appointed the new Roscosmos chief, replacing Vladimir Popovkin who lasted only 2.5 years at the post.
The replacement comes as Russia struggles to overhaul its space industry, and President Vladimir Putin yesterday approved the creation of a new state champion that will group together the country's aerospace makers.
"I am hoping that a whole number of problems, which unfortunately have been recently seen in Roscosmos' work, can be overcome with your arrival," Medvedev told Ostapenko, noting that his agency will remain in charge of the "ideology of space development".
Before his appointment to the post of deputy defence minister last year, Ostapenko served as commander of space forces and before that as chief of Plesetsk Cosmodrome.
The previous Roscosmos chief Popovkin was appointed to the job in April 2011 amid frustration in the government with the country's space programme including a series of satellite crashes and other setbacks.
However Popovkin's own stint was marked by continuing embarrassments including a spectacular explosion of an unmanned carrier rocket upon takeoff that was caught on live television in July.
In an effort to put an end to several years of setbacks, Putin yesterday approved the creation of a new state corporation called the United Rocket and Space Corporation.
Space analysts said it remained to be seen how the state space agency and the newly-created corporation will share responsibility.