The presidential decrees changed a deputy interior minister, appointed a new head of the ministry's economic security department and a new head of the organized crime and terrorism department, the Kremlin said without elaborating.
Oleg Safonov, a former aide to the presidential envoy to the country's southern districts, became deputy interior minister.
Sergei Meshcheryakov was dismissed as head of the economic security department and will now oversee the ministry department on fighting organized crime and terrorism.
He was replaced in the post by Yevgeny Shkolov, formerly a Kremlin administration member and a top manager at the state-owned Transneft pipeline monopoly.
And Vladislav Piotrovsky, chief of the criminal police and deputy head of the Interior Department of St. Petersburg and the region, was promoted to police chief in Russia's second city and adjacent districts.
A number of senior security officials and high-ranking customs officials have been fired, convicted or are still under investigation in Russia since Putin highlighted an anti-corruption campaign in his State of the Nation address in May.
He said corruption and rampant bureaucracy are the main problems holding back Russia's economy.
Russia ranked 121 in a new Corruption Perception Index report published by Transparency International last week, which placed it above Azerbaijan but below such ex-Soviet republics as Kazakhstan, Ukraine, Georgia, and Moldova.
Russia's Interior Minister Rashid Nurgaliyev said the number of corruption cases in the country rose to 35,000 in the past five years. "Bribery and bribe-taking alone have increased 40%," he said.