The press service said Dmitry Medvedev had signed an order dismissing Leonid Melamed, who was once Chubais's first deputy at Unified Energy Systems (UES), and giving the job to the former deputy prime minister.
Chubais, 53, had been widely expected to head the corporation - set up to promote nanotechnology research as part of the Kremlin's efforts to reduce the country's dependence on energy resources - since the breakup of UES, which he led for 10 years.
UES was broken up in July into a web of power generators as part of a large-scale reform to attract foreign investment to the decaying industry.
Chubais is a member of the corporation's supervisory board and of a government commission on high technology and innovation.
He is not, however, a popular figure in Russia, blamed first as a leading architect of the country's transition to capitalism that allowed a handful of oligarchs to earn fortunes in privatization deals in the 1990s, when millions were left in poverty amid persisting economic crisis, and latterly for raising electricity charges as UES sought to pass costs on to previously protected domestic consumers.
Chubais, an advocate of the free market, has been critical recently of the Russian government for increasing its role in the economy.