The missing cache of explosives has become a politically charged issue in the US election race, with Democratic challenger John Kerry accusing the Bush administration of failing to secure the site.
In a Washington Times story this week, Pentagon official John Shaw pointed the finger at Russian special forces, saying they had moved many of Iraq's weapons into Syria in the weeks before the March 2003 invasion.
"The Russian ministry of defence summoned the US military attache in Moscow to express a resolute protest in connection with the comments by John Shaw," Interfax quoted an anonymous source at a Russian defence agency as saying on Friday.
A spokesman at the US embassy in Moscow confirmed that a member of the embassy's defence staff had been "called in", but denied it was the chief military attache and declined to say what had been discussed at the meeting.
Russia's defence ministry dismissed the allegations that there had been any Russian involvement in the disappearance of the explosives in Iraq.
"You can't really take statements like this as anything but far-fetched rubbish"
Russian defence ministry
"You can't really take statements like this as anything but far-fetched rubbish," said spokesman Vyacheslav Sedov.
"I can officially confirm that the ministry of defence and the organisations that report to it could not have taken part in the disappearance of the explosives, since Russia's servicemen and military specialists left Iraq 12 years ago."
Bush and Pentagon officials have argued that Saddam Hussein's government may have moved the explosives from the al-Qaqaa storage site near Baghdad before the start of the war to protect it from US attack.
But US Defence Secretary Donald Rumsfeld has distanced himself from the comments by Shaw, who is deputy undersecretary for defence for international technology security.