Mr Bakradze said Russia's move was against all norms of international law
Georgia has accused Russia of trying to annex the breakaway republics of Abkhazia and South Ossetia with its decision to seek closer ties with them.
Moscow said it would intensify social and economic co-operation in the regions and recognise businesses and organisations registered there.
But Georgian Foreign Minister David Bakradze said this amounted to "de facto annexation" of its provinces.
Last month, both regions called on the UN to recognise their independence.
Tbilisi responded by warning Moscow not to take any step towards recognition.
A senior MP in the Georgian parliament, Shota Malashkhia, said it would lead Russian peacekeepers to be "outlawed" in Abkhazia and South Ossetia.
Russian and UN peacekeepers have been deployed in the two republics since the early 1990s, when violence broke out as both regions tried to break free from Georgian control.
EU foreign policy chief Javier Solana was said to be "concerned" by what were described as "these unilateral decisions".
"We have always supported Georgia's territorial integrity," his spokeswoman Christina Gallach said.
Georgian TV reported that the country's Security Council convened in emergency session.
Moscow said its decision to recognise some documents issued by the republics' authorities was in the interests of their mainly Russian citizens and was not intended to inflame the situation.
"Our actions with regard to Abkhazia and South Ossetia do not mean that Russia is making a choice in favour of confrontation with Georgia," a foreign ministry statement said.
Abkhazia's Foreign Minister Sergei Shamba said Russia's decision would lead to a "breakthrough" in resolving economic, social and security issues.