The protesters attacked the U.N.-escorted convoy as it was entering the village of Mala Krusa, some 70 kilometers (43 miles) southwest of province's capital, Pristina, police spokesman Fatmir Gjurgjeali said.
Three U.N. vehicles were damaged, and there were reports of protesters seeking medical help after police intervened with tear gas, Gjurgjeali said.
The incident will come as an embarrassment for the U.N. mission running this ethnically divided province, a day after it said that the rate of interethnic violence was falling.
Another police official said the U.N. police was escorting a convoy of Serbs in the ethnic Albanian village, which suffered major destruction and losses during the crackdown by Serb forces on independence-seeking ethnic Albanians, which left an estimated 10,000 people killed.
Some 105 ethnic Albanian men and boys were killed in Mala Krusa and another nearby village by Serb forces in 1999, some of the worst hit regions during the war here, the AP reports.
Tens of thousands of Serbs and other minorities have fled Kosovo in the war's aftermath, escaping revenge attacks by ethnic Albanians.
Though Kosovo's leadership has invited Serbs to come back to their original homes in the province, and international administrators have conditioned the province's possible independence with respect for minorities, some ethnic Albanians remain hostile to their return.
Still, nearly seven years since the end of the war, the ethnic groups remain divided, with Kosovo Serbs mainly living in isolated enclaves fearing attacks by ethnic Albanians.
Talks to determine Kosovo's future are underway in Austria. Western envoys hope that some form of solution will be found by the end of 2006, which should primarily ensure the well-being of minorities, particularly Serbs.
Chinese President Xi Jinping warned his new US counterpart Joe Biden not to push Europe into an alliance against Beijing