A spokesman said the evacuation of residents, thousands of whom have fled across the border to Russia since the start of Georgia's ground and air offensive three days ago, is continuing.
"We are evacuating people not because of armed hostilities - everything is under our control - but because the city is destroyed and its residents have nowhere to spend the night. They have nothing to eat or drink," he said.
He said South Ossetian soldiers and Russian peacekeepers have taken full control over Tskhinvali and surrounding villages.
South Ossetia's Press and Information said earlier on Monday Georgian forces had blown up a water treatment plant in Tskhinvali. Cellars in the western part of Tskhinvali, where civilians had taken shelter from the fighting, were subsequently flooded.