The children are being taken to Vladikavkaz, the capital of Russia's North Ossetia province, where they will be cared for by local authorities, Gagloyeva said.
Russia's NTV showed a large crowd of parents and children in a parking lot in Tskhinvali, South Ossetia's main city, before the buses departed for North Ossetia.
Brink of war
The decision to evacuate children was made after an eruption of violence late on Friday and early on Saturday, which included sniper and mortar fire between South Ossetian and Georgian forces. Six people died in the fighting.
Shota Utiashvili, a spokesman for Georgia's interior ministry, said the situation was relatively calm overnight, though the two sides exchanged sporadic automatic weapons fire.
Mikhail Saakashvili, the Georgian president, has promised to bring both breakaway provinces under Tbilisi's control.
But leaders of South Ossetia and Abkhazia say they will never submit and instead have insisted on independence or absorption into Russia.
Russia maintains a large peacekeeping contingent in each province.
Eduard Kokoity, the president of South Ossetia, suggested in a recent statement
posted on his website that North Ossetian brethren were prepared to rush to
the breakaway region's aid if the conflict continued to escalate.
At least six people were killed on Friday by mortar and sniper fire in the region, officials from the provincial government said.
Seven more were wounded when Georgian forces opened fire with rifles and mortars in Tskhinvali, the capital, the government said in a statement on Friday.
Georgia has denied initiating an exchange.
Kokoity told the Interfax news agency that the region's response to Tbilisi's "aggressive actions" would be "very tough and hard-hitting".
"We reserve the right to strike Georgian cities. We have something that can reach them."