According to Russian media, Korabelnikov had criticised reforms that aim to modernise Russia's army and nuclear arsenal.
The reforms would also see a reduction in the number of generals and personnel, making them deeply unpopular in the military.
'Message to generals'
The Kommersant newspaper reported last November that Korabelnikov was one of a group of generals who had submitted their resignations in protests over the reforms.
Viktor Ilyukhin, deputy leader of the opposition Communist party and former deputy head of parliament's national security committee, said Korabelnikov's dismissal was a "blow at our Russian forces and the security of our nation".
"He was a born intelligence chief, a man who brilliantly knows the situation in the world and one of the best experts in the situation in Russia's army," he told the Reuters news agency.
Analysts believe Medvedev may be trying to send a message to generals that he is not going to tolerate dissent on military reform.
Alexander Shlyakhturov, Korabelnikov's successor, was the sacked general's first deputy. He is seen as a more compliant figure who is less likely to challenge the reforms.
The GRU was created in 1918 under Leon Trotsky, and is controlled by the military general staff.
Since its creation it has been widely seen as a staunch rival of other spy agencies.