Since February 2005 he has been the Director of the Kurchatov Institute.
In June 2007 by a decision of the Russian Academy of Sciences Presidium Mikhail Kovalchuk was appointed acting vice-president of the Academy for nanotechnology. As the Academy Charter stipulates that only full members are eligible for vice-presidency, Kovalchuk, being an associate member, can only be acting vice-president, unless the charter is modified or he is elected full member.
Despite pressure from Vladimir Putin, the RAS rejected Kovalchuk's application for full membership in May 2008. This was seen as the first major blow to Putin's authority since coming to power in 2000 as Putin had wanted to appoint him President of the RAS.