Georgian and Russian troops fought a brief war in the region earlier this month and are now observing a fragile cease-fire.
Georgian officials said the village of Mosabruni was not part of separatist-controlled territory and alleged the separatists were planning a provocation against Georgian special forces who had been deployed there.
The separatist administration said the village was within South Ossetia and the Georgian forces were there unlawfully. It accused Tbilisi of massing armed men in preparation for an attack.
"According to our information, South Ossetian militias want to take this village. Our forces got the order not to shoot, but if Ossetians start shooting they will have to return fire," Alexandre Lomaia, secretary of Georgia's National Security Council, told Reuters.
Lomaia said the atmosphere in the majority Georgian-populated village was "very tense." He declined to say exactly when Georgian forces had returned there.
Although the village lies just inside the region of South Ossetia, it has been under Georgian control for over a decade and is considered by Georgia as part of its territory.
"We believe that the Ossetians are preparing a provocation there," Lomaia said.
A separatist official said the village, 70 kilometers west of the regional capital, Tskhinvali, lies inside South Ossetia, and the separatists were consulting Russian forces on their next move.
"About three hours ago, Georgian policemen occupied the village of Mosabruni. They told locals to leave straight away. Villagers are leaving on foot," Irina Gagloyeva, head of the separatists' Committee for Press and Information, told Reuters. "South Ossetian security bodies are now holding consultations with Russian peacekeepers and I hope very much they will not allow a new flare-up."
In a second South Ossetian village, Mugut, separatist forces detained a group of Georgian policemen, Interfax quoted separatist officials as saying.
Georgia says its cease-fire agreement with Russia allows Georgian police return to all areas where they were present before the conflict, including villages such as Mosabruni.