Georgia said Russia's establishment of closer links with the regions was against international law.
Bakradze said it "can be assessed by the Georgian side only as a legalisation of the de facto annexation process which has been taking place in two Georgian regions".
Saakashvili has vowed to restore central control over the two breakaway territories which threw off Tbilisi's control in fighting in the 1990s.
Putin also instructed his government to accept identification documents issued by the separatists, recognise businesses and organisations registered under Abkhaz and South Ossetian law, and look at providing consular services to residents in the two regions.
|"I am deeply concerned by the actions Russia has taken to establish legal links with the Georgian regions of Abkhazia and South Ossetia" |
Jaap de Hoop Scheffer, Nato secretary-general
The statement made no mention of Russia recognising the two regions' claims for independence from Georgia.
Nato has said it is deeply concerned by Russia's announcement and asked Moscow to reverse the move.
"I am deeply concerned by the actions Russia has taken to establish legal links with the Georgian regions of Abkhazia and South Ossetia," Jaap de Hoop Scheffer, Nato secretary-general, said.
"I urge the Russian Federation to reverse these measures, and call on the Georgian authorities to continue to show restraint."
Sergei Shamba, Abkhazia's separatist foreign minister, said Putin's order was a step towards independence for the region.
"In effect, Abkhazia is in the final straight before the finishing line, beyond which lies the recognition of our independence," the Russian news agency Interfax quoted him as saying.
Russia's foreign ministry said in a statement on its website that the decision to set up legal links with the separatists was motivated by a desire to protect residents there, many of whom are Russian passport holders.
The statement said: "Our actions with regard to Abkhazia and South Ossetia do not mean that Russia is making a choice in favour of confrontation with Georgia.
"Implementation of these measures will facilitate the strengthening of security and stability in the Caucasus region."
Moscow had previously warned that it would respond to any recognition of Kosovo, which declared independence from Russia's ally Serbia in February, by stepping up its relations with Abkhazia and South Ossetia.
Some Russian officials have also linked the issue to an application by Georgia's leadership to join Nato.
The military alliance agreed at its summit this month, in the face of fierce Russian opposition, that Georgia would eventually be allowed to join.
"Russia is wary of Nato's eastward expansion, and wary too of losing total control and influence of a country like Georgia on Russia's borders," Jonah Hull, Al Jazeera's correspondent in Moscow, said.
"So, fomenting or encouraging instability on the border in these regions of Georgia is a very good way of making Georgia seem like a less palatable prospect for Nato."
"Saakashvili has offered limited autonomy for Abkhazia, he has even offered a so-called vice-president with veto powers over any decisions taken by Tblisi."
Although separatists in Abkhazia and South Ossetia threw off Georgian control during fighting in the 1990s, Georgia has vowed to restore its rule and on paper they are still officially part of the state.
The Russian government has never recognised the two republics, but has granted citizenship to hundreds of thousands residents of the region.