However, it said most EU members had taken a 'responsible approach' to partnership with Russia.
At its summit in Brussels, the EU postponed talks on a new partnership deal with Russia until it pulls it troops out of Georgia.
While the 27-nation organization stopped short of imposing sanctions, it also pledged to strengthen economic and political ties with Georgia, and condemned Russia's decision to recognize South Ossetia and Abkhazia.
"The majority of EU member states have shown a responsible approach, confirming the course toward partnership with Russia, in full awareness of the importance of mutually beneficial cooperation," the ministry said.
It also said Moscow could not possibly agree with a number of 'prejudiced' points in the EU declaration, including one concerning Russia's 'disproportionate' reaction to Georgia's attack on South Ossetia on August 8 during which hundreds of civilians died and thousands were forced to flee to region.
It also regretted the fact that the EU had failed to realistically assess the role of "those who have supplied Georgia with arms, in violation of OSCE and EU rules."
The ministry said Russia's partnership with the EU "must not become hostage to differences in opinion on specific issues."
Russia earlier rejected the EU declaration, saying it sent the "wrong political signals".
A new round of talks on a Russia-EU Partnership Cooperation Agreement governing trade, military and energy relations were due to start on September 15. Talks had been launched in July after 18 months of delays. Relations are still governed by an accord signed in 1997.
Britain, Poland, and the ex-Soviet Baltic states had led calls for tough measures against Russia in the run-up to the summit, while France, Italy, Germany, Spain and Finland had taken a more cautious stance, warning against damaging ties with Russia.
The EU also agreed on Monday to send a fact-finding mission to the region, and pledged to strengthen ties with Tbilisi and provide financial aid for reconstruction.
Russia officially recognized South Ossetia and Abkhazia on August 26, saying the move was needed to protect the regions following Georgia's attack on South Ossetia.
