Police in Banja Luka responded by firing tear gas and water cannon at the hundreds of protesters, who oppose reconstruction of the 16th century Ferhadija mosque destroyed by Serbs during the 1992-1995 Bosnian war.
The clashes left one policeman in serious condition and a dozen others slightly injured, said Drago Gasesa, a Bosnian Serb police official. More than 60 demonstrators were arrested.
It was the second time demonstrators had tried to disrupt the cornerstone-laying ceremony in Banja Luka, the administrative center for the Serb-run half of the country.
Despite Monday's demonstration, the ceremony was completed this time.
During the war, Serbs expelled Muslims from Banja Luka and destroyed all the city's mosques including its most famous, the Ferhadija mosque. The 16th century mosque was declared a worldwide cultural heritage monument by UNESCO.
International officials ordered the mosque's reconstruction as part of efforts to foster reconciliation and encourage refugees to return.
Police had warned demonstrators Monday they would be videotaped and that the tapes would be used as evidence if crimes were committed.
The 1995 peace accords left Bosnia formally one nation, but split it into a Serb half and another shared by Croats and Muslims.
Banja Luka, in northwest Bosnia, is the heartland of the Bosnian Serb republic, where most Muslim and Croat residents were expelled in violent wartime ethnic cleansing campaigns. Many local people fiercely oppose the return of non-Serbs.
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