In a statement issued at a EU foreign ministers' meeting in Brussels today, the EU said the November 12 vote did not contribute to efforts to resolve the conflict peacefully.
The EU ministers were to hold talks later today with Georgia's Prime Minister Zurab Noghaideli.
South Ossetia broke away from Georgia in a bloody war in the early 1990s.
Election officials in South Ossetia, citing preliminary results, today said 99 percent of the territory's registered Ossetian residents have voted for independence.
The OSCE and the Council of Europe also reiterated today they will not recognize the referendum and condemned it as unproductive.