Georgia is seeking to regain control of Abkhazia and South Ossetia, which proclaimed independence following the break up of the Soviet Union in 1991. Tbilisi accuses Moscow of encouraging separatism and interfering in its internal affairs.
"The Russian president stressed that Russia is not unsympathetic to the aspirations and problems to the two republics' population, where many Russian nationals live," the ministry said.
Earlier the presidents of the two breakaway republics expressed in a statement to Putin their concerns over the "aggressive course by the Georgian authorities to destabilize the situation in the conflict zones, Georgia's militarization, the build up of offensive weapons and troops close to the borders of the [self-proclaimed] republics."
The Russian president said that all Georgia's attempts to resolve the situation by applying pressure on Abkhazia and South Ossetia are senseless.
"Any attempts to apply political, economic or especially military pressure on Abkhazia and South Ossetia are futile and counterproductive," the ministry said citing Putin.
Sergei Bagapsh, the president of Abkhazia, said in an interview with RIA Novosti that Putin's statement would "guarantee security for our republics. This is how I understood it."
Two weeks ago the State Duma, Russia's lower house of parliament, proposed that the president and the government consider the issue of whether to recognize the independence of Abkhazia and South Ossetia.
Ex-Soviet breakaway regions have stepped up their drive for independence since Kosovo's declaration of independence on February 17. Abkhazia and South Ossetia, along with Moldova's Transdnestr, have since asked Russia's parliament, the United Nations and other organizations to recognize their independence.
Peacekeeping in the Georgian-Abkhaz conflict zone is currently carried out by collective CIS forces staffed with Russian service personnel. The Georgian-South Ossetian conflict area is controlled by joint forces also including Russian peacekeepers.