The EU called on officials in Pristina and Belgrade to end the hostilities immediately, EUobserver reported.
"Violence will never be tolerated and unilateral actions are not the way forward," EU foreign policy chief Catherine Ashton said Wednesday, telling Serbian President Boris Tadic and Kosovo Prime Minister Hashim Thaci to "underline their responsibilities."
"It is now critical for both sides to return to dialogue, and to resolve the underlying issues without delay," Ashton said.
Fighting broke out Monday after the government in Pristina ordered special forces troops to set up border check points in the mostly Serb populated regions in the north to enforce a recent trade embargo with Serbia.
That move angered ethnic Serbs, who subsequently set up barricades and opened fire at Kosovo police officers, killing one. Dissidents also set fire to some border posts, the report said.
NATO troops and the European Union's police force, Eulex, intervened, but said Wednesday evening the checkpoint in Jarinje, in northern Kosovo, was set on fire. NATO said its troops were shot at.
"It was confirmed that an act of arson was committed against that position … there have also been confirmed reports of shots fired at Kfor [NATO] personnel in the vicinity," Kfor said in a statement.
Officials in Pristina said the attack was masterminded in Belgrade by Serbs who want to take a piece of northern Kosovo.
"This will never happen," Thaci said.
Tadic condemned the violence and urged Kosovo Serbs from taking part.
"The hooligans who are sparking violence are not defending either the people or the Serb state," Tadic said.