The ministry said in a Tuesday statement that the launch of the facility near Iran's holy city of Qom demonstrated that Tehran was continuing to ignore international concerns about its nuclear program.
It added, however, that Iran had notified the International Atomic Energy Agency in due time of the launch of the bunker facility.
The ministry says Russia was urging all parties involved in the Iranian nuclear standoff to avoid "ill-considered and abrupt moves," which could undermine prospects for talks with Iran.