"[General Anatoly] Mazurkevich was dismissed from office some time ago, and his department is undergoing financial checks," the source said. "The checks have been ordered by the ministry's top officials."
Mazurkevich, who Russian daily Nezavisimaya described as a former intelligence officer and who was appointed to the post in 2001 by then Defense Minister Sergei Ivanov, has been unavailable for comment.
The ministry has also made no comment on the dismissal, which was preceded by the firing of several other officials from the department for international military cooperation.
President Vladimir Putin set the fight against corruption among government ranks a national priority in July 2005. Hundreds of probes, including against senior military, security, police and justice officials, have been opened since then.