Initial results from the first election in Sri Lanka since the civil war ended in May show the governing party has taken Jaffna, the region's biggest city.
But it suffered a surprise defeat in Vavuniya, the other town where polling took place, where a group supportive of the defeated Tamil Tiger rebels won.
Ballots are still being counted in the southern province of Uva.
The BBC reports voters in had a choice between a broad government coalition, the main opposition party, which is weaker, and an umbrella group supportive of the Liberation Tigers of Tamil Eelam.
Turnout was low - 20% in Jaffna and 52% in Vavuniya.
As a result of its victory in the civil war, the government is very popular in the south.