The ministry said that violence against Russians in Abkhazia and South Ossetia, breakaway Georgian provinces, would be met with tough reprisals from the Russian side.
"Any attempts by Georgia to use force to resolve the conflicts, or to employ violent measures against Russian peacekeepers or Russian citizens living in Abkhazia and South Ossetia will encounter an appropriate and tough response," the ministry said in a statement.
The statement said Georgian aggression has forced Russia to increase peacekeeping numbers in the conflict zones.
Russia's Foreign Ministry said on Tuesday that Georgia is preparing to launch a military operation against Abkhazia.
Georgia is amassing troops, weaponry, ammunition, food and material supplies in the upper Kodori region on the border with Abkhazia, the statement said.
"The number of troops and police exceeds 1,500... The composition of the contingent indicates that Georgia is preparing to launch a military operation against Abkhazia," the ministry said.
Abkhazia and South Ossetia broke away from Georgia in 1991 following the collapse of the Soviet Union. Georgia is looking to regain control over the two republics.
Russian President Vladimir Putin called earlier this month for closer ties with the breakaway republics. Putin's statement provoked an angry response from Tbilisi, which accused Russia of attempting to annex the two republics.
Georgia also claims that on April 20 a Russian MiG-29 Fulcrum fighter from the Gudauta military base in Abkhazia, where Russian peacekeepers have been stationed since the end of a bloody conflict in the early 1990s, shot down a Georgian drone, a claim Russia has denied.
The incidents have seen relations between Moscow and Tbilisi plunge to a new low.
Ex-Soviet breakaway regions have stepped up their drives for self-rule since Kosovo's unilateral declaration of independence from Serbia on February 17. Abkhazia and South Ossetia, along with Moldova's Transdnestr, have all asked Russia's parliament, the UN, and other organizations to recognize their independence.
