"A new escalation in the South Caucasus is causing concern," the ministry's information and press department said.
A car bomb went off on Friday in the capital of South Ossetia, Tskhinvali, killing seven Russian peacekeepers. Georgia has denied any involvement in the bombing, accusing Russia of trying to delay its pullout from the buffer zone near South Ossetia.
The ministry said that Russian Foreign Minister Sergei Lavrov has sent a letter to his French counterpart Bernard Kouchner outlining "Russia's concerns regarding the provocation and deteriorating situation in the security zone."
However, the ministry said that despite the worsening security position, Russia intends to withdraw its peacekeepers from Georgia by October 10.
"Nevertheless, we firmly intend to fulfill the obligations agreed between the Russian and French presidents on the withdrawal of Russian peacekeepers from Georgia on October 10, 2008," the ministry said.
Under an EU-brokered peace deal, Russia has pledged to pull all troops out of the undisputed parts of Georgia within one month, leaving peacekeepers in South Ossetia and Abkhazia, which Moscow has recognized as independent countries. Russia has agreed to pull all its remaining peacekeepers out of the area by October 10.
Moscow launched a five-day operation to "force Georgia to accept peace" after Tbilisi attacked South Ossetia on August 8 in an attempt to regain control over the republic, which split from Georgia in the early 1990s. A number of Russian peacekeepers and a reported 1,600 South Ossetian residents lost their lives during the conflict.