Russia lost three satellites when a rocket crashed into the Pacific Ocean.
Prime Minister Vladimir Putin removed Mr Perminov, 65, because he had "reached the age limit for civil servants", a government statement said.
First Deputy Defence Minister Vladimir Popovkin will now head the federal space agency, Roscosmos.
In December President Dmitry Medvedev fired Roscosmos deputy chief Viktor Remishevsky and Vyacheslav Filin, deputy head of the space rocket corporation Energia, over the loss of the three Glonass-M navigation satellites. He also reprimanded Mr Perminov.
An inquiry showed the Proton-M rocket failed to reach orbit because of a fuel miscalculation.
Earlier this month Russia celebrated the 50th anniversary of the first human spaceflight by Soviet cosmonaut Yuri Gagarin.
