The president appointed Korabelnikov's first deputy, Lt. Gen. Alexander Shlyakhturov, as the new military intelligence chief and deputy chief of the General Staff.
Media reports earlier claimed that Korabelnikov, 63, who has led GRU since May 1997, had tendered his resignation over objections to a proposed reform of the body, but Russian military officials have consistently dismissed the rumors, saying the general would keep his post for another two years until he reached retirement age.
A GRU source told RIA Novosti on Friday that Korabelnikov had tendered his resignation several times, but only the latest request had been satisfied.
"Korabelnikov recently submitted another request for retirement to protest the ongoing disbandment and re-subordination of elite GRU divisions and also some steps to streamline the GRU structure," the source said.
GRU is Russia's largest intelligence agency. It gathers human intelligence through military attaches and foreign agents. According to some sources, GRU has six times as many agents in foreign countries as the SVR, which is the KGB's foreign intelligence successor.
It also maintains significant signals intelligence and imagery reconnaissance and satellite imagery capabilities.