It was the first time voters in all of Kosovo were choosing local leaders since the country seceded from Serbia in 2008.
The vote was seen as a key test of whether ethnic Serb-majority areas in the north who have rejected the ethnic Albanian government's authority would cast ballots, but hard-liners are suspected of smashing up a polling station to intimidate fellow Serbs from voting.
Prime Minister Hashim Thaci maintained the Serb-majority areas now have "legitimate representatives," even though election authorities have not yet decided whether to count the results. Enough ethnic Serbs turned out there and elsewhere around the country to give them a voice, he said.
He said voter turnout in the Serb-run north was 22 per cent before the attack.
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Serbs in the rest of Kosovo marked a record turnout in some areas with over 50 per cent of voters casting ballots.
A group of masked men broke windows and tore up voting materials at a polling station in the northern town of Mitrovica on Sunday, forcing the closure of the voting station and evacuation of members of the Organization for Security and Cooperation in Europe, which provided technical support for the vote.
"We were not able due to the attack on the polling center to take custody and protect those materials," Gaon said.
The votes from the rest of northern Kosovo are not being processed until there is a decision on what to do with the ones at the Mitrovica polling station, election officials say.
Participation of minority Serbs in the elections was a key element in an EU-brokered deal between Serbia and Kosovo that seeks to settle longstanding disputes. Serbia does not recognize Kosovo's independence.
In Belgrade, Serbia's minister for Kosovo said the government is waiting to hear from election officials before taking a stance. He said Serbia will punish any of its citizens who took part in the violence.
"The election boycott has failed," said Aleksandar Vulin. "One polling station does not represent all Serbs in Kosovo.