It said Russia had received information indicating that Georgian troops were preparing a military operation into the region which, along with Abkhazia, has had de facto indpendence since a separatist conflict in the 1990s.
"As subsequent events showed, this step allowed [us] to cool hot heads in Tbilisi and prevent events developing along military lines, the likelihood of which was more than real," a Russian statement said.
Earlier in the week Russian peacekeepers deployed in the region claimed it was Tbilisi that had violated the no-fly zone which is in place as part of a ceasefire agreement.
The statement is Russia's first admission for at least a decade that its air force has flown over Georgian territory.
|Russia said its jets had flown over South Ossetia earlier this week [GALLO/GETTY]
Separately, Sergei Lavrov, Russia's foreign minister, held talks with the leader of Abkhazia's separatist government.
Georgia's government is locked in a confrontation with Russia over the breakaway regions which enjoy considerable support from Moscow.
Condoleezza Rice, the US secretary of state, on Thursday urged Russia to help resolve tension in Georgia's rebel regions rather than "contributing to it".
"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 said at a news conference with Mikheil Saakashvili, Georgia's president.
"The violence needs to stop and whoever is perpetrating it, and I have mentioned this to the president, there should not be violence."
Rice also reaffirmed Washington's support for Georgia's bid to join Nato.|
Saakashvili said Russian fighter jets had come close to the Georgian capital late on Tuesday.
"Maybe they wanted to salute secretary Rice," he said. "I don't know ... This is a very worrisome development."
Saakashvili said Russia's behaviour was a reaction to Nato expansion and an increasing US presence in the region.
"Looks like some people did not notice that the Cold War is over. The main point is that Russia ... no longer acknowledges the jurisdiction of Georgia towards an essential part of its territory," he said.
In the worst violence in months, a bomb in a cafe in Abkhazia killed four people on Sunday and separatists in South Ossetia said two people were killed last week in a heavy exchange of fire with Georgian forces.
Russia said there was strong evidence Georgia's government was behind the violence, although Tbilisi has denied the allegations.