The move came shortly after Russia admitted it had sent aircraft to monitor the situation in South Ossetia earlier this week due to fears of a Georgian invasion of the de facto independent republic.
"We are very much indignant at Russia's aggressive policy. We will take some forceful diplomatic steps in order to respond adequately to Russia's actions. From today, we are recalling our ambassador in Russia for consultations," Yekaterina Tkeshelashvili said.
Earlier in the day, the Georgian Foreign Ministry summoned Alexander Smagu, the minister-counselor at the Russian Embassy in Tbilisi, and handed him a note of protest in connection with the recent flights.
A senior Georgian Air Force official said on Wednesday that two Russian fighters had flown into Georgian airspace and were later joined by two other aircraft. Russia also said that Georgia had sent fighters to the conflict zone on Tuesday.
South Ossetia and another Georgian breakaway republic, Abkhazia, have been the source of rising tensions between Georgia and Russia of late. Moscow recently moved to establish closer ties with the separatist regions and sent additional peacekeepers into Abkhazia, saying they were needed to deter "new bloodshed."
Georgia has accused Moscow of trying to annex its territory.
Four people were killed in an explosion in a cafe in Abkhazia on Sunday, and two more died in a clash with Georgian troops in South Ossetia last week.
U.S. Secretary of State Condoleezza Rice said during her visit to Georgia on Thursday that Russia should help Georgia resolve conflicts with its breakaway regions rather than exacerbate them, and urged the countries to refrain from violence.
"It [Russia] needs to be a part of resolving the problem and solving the problem and not contributing to it. I have said it to the Russians publicly. I have said it privately," she told a news conference in Tbilisi.