It did not give a reason for the dismissal or say who would replace him.
Putin appointed former Prosecutor General Vladimir Ustinov as Russia's justice minister in late June.
Ustinov, 53, was removed from the prosecutor's office June 2 in what senior officials said at the time was a planned staff rotation bereft of political intrigue. Speculation soon followed that he would be given another senior position.
Ustinov's time in office was dominated by the Yukos case, which culminated in the virtual dismemberment of the oil company and the imprisonment of founder Mikhail Khodorkovsky, for tax evasion and fraud.
A number of senior security officers from the Federal Security Service and high-ranking officials from the Federal Customs Service have been fired since Putin highlighted an anti-corruption campaign in his May 10 state of the nation address.