The order is included in President Vladimir Putin's "instructions to the government concerning Russia's relations with Abkhazia and South Ossetia," the ministry said in a statement and follows Russia's move to lift trade restrictions in the two breakaway republics.
The Foreign Ministry also said Russia would provide consular services for Abkhazians and South Ossetians, many of whom are Russian passport holders, in Russia's southern Krasnodar Territory and North Ossetia.
The ministry said, however, that in developing relations with Georgia's breakaway republics, Russia does not want confrontation with Tbilisi.
"Our actions regarding Abkhazia and South Ossetia do not mean Russia is choosing [the path of] confrontation with Georgia. We are in favor of lifting all sanctions and restrictions hindering the region's social and economic development. This is confirmed by the resumption in air and sea links with Georgia and other steps," the ministry said.
The chairman of Georgia's parliamentary committee on defense and security, Konstantin Gabashvili, said Wednesday the Georgian Security Council would meet soon to work out Tbilisi's response to the Russian measures.
"Response measures will be developed. The situation will be analyzed. We will take steps on our side, I will not specify what," he said. "Russia's actions look like aggression. Moscow is virtually trying to annex Georgian territories."
Georgia is seeking to regain control of Abkhazia and South Ossetia, which proclaimed independence following the break-up of the Soviet Union in 1991.
Georgian President Mikheil Saakashvili instructed the government on Saturday to work out a plan for the implementation of his initiatives aimed at granting Abkhazia broad autonomy and establishing a free economic zone in the separatist province, but Abkhazia once again rejected the offer.
Saakashvili first offered Abkhazia unlimited autonomy and the post of a vice-premier for the Abkhaz leader in his March 28 speech, which was rejected by the Abkhaz President Sergei Bagapsh.
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 UN and other organizations to recognize their independence.
The Russian Foreign Ministry said Georgia's new proposal to Abkhazia could not be regarded as serious.
"The refusal by the Georgian leadership to conclude binding documents with Sukhumi and Tskhinvali on the non-use of force and non-resumption of military action....is in violation of UN Security Council resolutions," the ministry said.
The South Ossetian foreign minister, Murat Dzhioyev, said Wednesday Putin's instructions to the Russian government demonstrate that Russia has begun the process of recognizing independence of these republics.
The Federation Council of Russia's upper house will debate recognizing the two republics on April 25, the speaker said on Wednesday. The question was first discussed by Russia's lower house in March.
"By this date we will have drafted a resolution giving the principal and balanced position of the state on this issue," Sergei Mironov said.
In their statement, supported by 441 votes out of 450, Russian MPs said it was necessary to protect people in Abkhazia and South Ossetia from a possible invasion by Georgia or from Georgia's potential accession to NATO.
