Irakly Okruashvili, the Georgian defence minister, said his helicopter was shot at by "the Ossetian bands" and had been forced to make an emergency landing.
He and the crew escaped unharmed.
Zurab Nogaideli, the Georgian prime minister, told Georgia's Rustavi-2 television: "This is yet another provocation out of the many already staged by the regime in Tskhinvali [South Ossetia's centre] and the military command of Russian peacekeepers deployed in the zone of the Georgian-Ossetian conflict."
Shots were fired at the Georgian helicopter, but it managed to land on territory controlled by the Georgian side.
Georgia's independent Imedi television channel showed Okruashvili saying the helicopter was carrying him to Senaki in western Georgia.
He said: "For 10 to 15 minutes, we were actually plunging. But the experience of the pilot saved the helicopter."
Video footage showed the Soviet-era Mi-8 military transport helicopter with several bullet holes on one of its sides.
Source of tension
South Ossetia is a mountainous enclave on the Russian border which broke free from Georgia's rule in 1991 after a brief conflict.
It has a mostly ethnic Russian population and seeks closer ties with Russia, which gives it financial support.
The region is a frequent source of tension between Moscow and Tbilisi.
Georgia accuses Russia of propping up the breakaway rulers. South Ossetia's population are eligible for Russian passports.
Georgian President Mikhail Saakashvili has pledged to regain control over South Ossetia and another breakaway region, Abkhazia.
Recent bombings in South Ossetia in July have been blamed on Georgia, prompting the Russian government to warn the country against any further attacks on the region and to pledge that it would defend its peacekeepers and citizens in the region "by any means".
A joint peacekeeping force of Russians and Georgians is deployed in the region.