Putin's order calls for increased economic cooperation but stops short of formally recognizing the republics, which have enjoyed de facto independence since a series of separatist wars rocked the region in the early 1990s.
Putin told the government to "cooperate with the de facto authorities in Abkhazia and South Ossetia, including the organization of trade, economic, social and scientific cooperation," according to a statement posted Wednesday on the Foreign Ministry's web site.
The order is aimed at strengthening security and stability in the Caucasus and does "not mean that Russia is making a choice in favor of confrontation with Georgia," the statement said.
But Georgian officials criticized the order as a violation of international law, and the country's pro-Western president, Mikheil Saakashvili, convened an emergency session of his national security council.
Georgian Reintegration Minister Temur Iakobashvili, the official in charge of relations with Abkhazia and South Ossetia, said Putin's decision was part of the "creeping annexation" of his country's territories by Russia.
Iakobashvili called on the international community to help mediate the dispute. "I think that we should still rely on our international friends and exploit that opportunity first, and then we'll see," he said, speaking by telephone from London.
Previously, Iakobashvili said Georgia would use military force to regain control of the regions if Moscow recognized their independence.
"If the Russian government recognizes the regions, we would move to regain control by other means," he said during an interview with The Moscow Times in March. "Military means."
Following the security council meeting, Georgian Foreign Minister David Bakradze called the Russian decision illegal in an interview with Reuters.
"That is against all the norms of international law, and the Georgian side will do whatever it can do in order to bring diplomatic, political and legal response to this policy," he was quoted as saying.
Georgia received support from the United States and Europe.
"Our commitment to Georgia's territorial integrity and sovereignty is unshakable," U.S. State Department spokesman Sean McCormack told reporters in Washington.
Saakashvili also reached out to Europe for support, placing an emergency call to European Union foreign policy chief Javier Solana, said Cristina Gallach, a spokeswoman for Solana.
"Mr. Solana is concerned," Gallach said by telephone from Brussels. "Of course, the concern is the unilateral nature of the decision. Mr. Solana's position is that the EU has repeatedly stated that territorial integrity is important and he feels that such issues should be solved through dialogue."
In South Ossetia, a spokeswoman for the separatist government welcomed Putin's move, saying it would ease economic hardships in the stagnating region.
"As for Georgia, we don't care about their reaction any more. The main thing is to avoid any armed clashes," Irina Gagloyeva said by telephone from Tskhinvali, Reuters reported.
Abkhazia and South Ossetia maintain close ties to Russia.
Some two-thirds of Abkhazia's residents have Russian citizenship, although Georgia considers it an integral part of the country and has attempted to lure it back with a combination of threats and incentives.
Late last month, Georgia's United Nations ambassador, Irakli Alasania, offered Abkhazia "unlimited autonomy" within its borders, The Associated Press reported.
Relations between Russia and Georgia hit a crisis point in October 2006, when Tbilisi arrested and expelled four Russian military officers whom it accused of spying, and Moscow responded by severing road and air links with Georgia.
Tensions between the countries seemed to ease in recent months. After Saakashvili met with Putin in Moscow in February, road and air links were reopened.
Since Kosovo declared independence from Serbia in March, however, Russia has been holding out the possibility of recognizing the rebel governments.
Moscow fiercely opposed the decision to recognize Kosovo's independence by the United States and some other Western countries. Russian officials have said that if Kosovo has its independence recognized, then so should Abkhazia and South Ossetia.
Russian lawmakers have backed the two breakaway republics. In a nonbinding vote in March, the State Duma voted 440-0 to recognize their independence. The Federation Council is set to vote on the matter April 25, Interfax reported Wednesday.
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