Medvedev dismissed Nikolai Kolesov, 52, and recommended the regional legislature consider Oleg Kozhemyako, 46, an aide to the chief of the presidential administration, as the new governor for the resources-rich region, the Kremlin said.
Media reports earlier said more than 10 investigations into corruption, fraud and abuse of office had been opened against members of Kolesov's team, some of whom have been arrested.
The governor, who was nominated by then president and now Prime Minister Vladimir Putin in June 2007, himself has been accused of underfunding local ministries and welfare programs.
Prosecutors were reported to be inquiring into the illegal construction of a country house by the former governor on the site of a nature reserve.
Local communists, nationalists and liberals held protest meetings in the summer demanding the dismissal of Kolesov and his team. And the Communist Party's local branch wrote a letter to the president saying the governor's policies "discredit the government and undermine respect for state authorities in society," media reported.
The governor's office dismissed the protests and the petition as the opposition's attempts to gain political weight.
Kolesov was approved for the post of governor in the Amur Region just two months after former governor Leonid Korotkov was dismissed from his position over abuse of office allegations.
Prosecutors accused him of raising electricity rates to illegally bankroll the local soccer team, buying vehicles at inflated prices and paying 16 million rubles ($620,000) to a mining company for a controlling stake that was never transferred to the regional government.