By Adam Tanner
CETINJE, Montenegro, Oct 17 (Reuters) - War is inevitable again one day in the Balkans because of the conditions faced by the Serb minority in Kosovo, the acting head of the Serbian Orthodox Church said.
Metropolitan Amfilohije Radovic's comments contrasted with the views of many political leaders who say the wars fought in the region in the 1990s are unlikely to be reignited as the former Yugoslav republics seek European Union membership.
Kosovo declared independence from Serbia on Feb. 17. Amfilohije said Kosovo's Serbs face hostility from the mainly Muslim ethnic Albanians, who make up about 90 percent of the population.
"Amid such injustice, there cannot be peace," Amfilohije said in an interview late on Thursday at his headquarters in the Monastery of Cetinje in Montenegro. "It will be the root of future conflict, that is as clear as the day."
He said he wanted peace but was "realistic".
"There will be some period of peace, but it will be a time that prepares for new conflict, new war, new struggle," he said.
Kosovo is the cradle of the Serbian Orthodox Church. Its declaration of independence has been recognised by almost 50 countries but angered Serbia, which has not recognised it.
Serbia lost control of its southern province in 1999, when NATO intervened to halt the ethnic cleansing of civilians in a counter-insurgency war, and the United Nations took over.
About 120,000 Serbs live in Kosovo and refuse to take orders from Albanian-run institutions. Ethnic Albanian leaders in Kosovo accuse Serbian leaders of trying to stoke instability.
Amfilohije became acting head of the Serbian Orthodox Church when Patriarch Pavle stepped aside for health reasons this year. He is considered a conservative who could become patriarch.
The Serb Orthodox Church offered prayers and moral support for Serb forces during the 1990s wars, but the Metropolitan said the church only had a pastoral role and did not act wrongly.
Amfilohije visited Radovan Karadzic, the Bosnian Serbs' political leader during the 1992-95 Bosnian war, in prison in Belgrade this summer before Karadzic's extradition to The Hague to face war crimes charges.
Amfilohije praised Karadzic as a "good man" but said the church had never sheltered him or Ratko Mladic, the wartime commander of the Bosnian Serb army who is still on the run.
(Editing by Timothy Heritage)