* Ex-rebels alleged to have taken organs from Serbs
* Kosovo government, led by ex-guerrilla, rejects charges
* Concerns over witness intimidation in Kosovo
By Fatos Bytyci
PRISTINA, April 4 (Reuters) - Plans are under way for a European Union-backed special tribunal to try Kosovo Albanian former guerrillas accused of harvesting organs from murdered Serbs during the Balkan country's 1998-99 war, officials say.
The move stems from a 2011 report by Council of Europe rapporteur Dick Marty alleging guerrillas fighting a war of independence from Serbia had smuggled Serb victims into northern Albania and removed their organs for sale.
Kosovo's government, led by former guerrilla commander Hashim Thaci, has angrily rejected the accusations as an attempt to tarnish the reputation of the Kosovo Liberation Army (KLA) rebels, who won NATO air support in 1999 to drive out Serbian forces.
Efforts to investigate alleged war crimes committed by the guerrillas have run up against widespread intimidation in a small country where clan loyalties run deep and KLA rebels are revered as heroes. Many entered government after the war, leading Kosovo to independence in 2008.
In an interview with Saturday's edition of the Kosovo daily Koha Ditore, Jonathan Moore, director of the U.S. State Department's Office of South-Central European Affairs, said preparations were under way with EU participation for a court based in Kosovo, "but where the best majority of the work is done outside Kosovo".
That may mean witnesses giving testimony abroad to protect them against attack or intimidation. Other major war crimes cases stemming from the collapse of Yugoslavia in the 1990s have been tried at a United Nations tribunal in The Hague.
Reuters was given an advance copy of Moore's interview.
The Kosovo government has resisted efforts to try suspects in the organ harvesting case outside Kosovo.
The allegations are being investigated by U.S. prosecutor John Clint Williamson on behalf of the EU, which has a mission in Kosovo overseeing major war crimes and corruption cases.
Williamson is expected to wrap up his work within months. A spokesman would not be drawn on plans to create a tribunal.
"We will either file an indictment or issue a finding that there is insufficient evidence to substantiate allegations contained in the CoE report of 2011," said Joao Sousa, spokesman for Williamson's EU-created Special Investigative Task Force.
"We have said from the outset that we expect to conclude our investigation in 2014, but it would be inappropriate for us to provide any more specific timings at this point," Sousa said.
Political sources say Western diplomats have been pressing the government to accept the tribunal and endorse it in a parliamentary vote.
Kosovo President Atifete Jahjaga, a former police officer with no political affiliation, spoke to Moore by phone on Friday.
"This process is focused on individuals and is not about putting on trial our joint efforts to liberate the country," her office said in a statement, in reference to the U.S.-led NATO bombing campaign in 1999 to drive out Serbian forces and halt the killing and expulsion of Kosovo Albanian civilians.
An estimated 10,000 people died during the war, the large majority of them ethnic Albanians. Hundreds of thousands of ethnic Albanians were driven from the then southern Serbian province into refugee camps, forcing the West to act against under Serbian strongman Slobodan Milosevic to halt further bloodshed following wars in Croatia and Bosnia.
About 1,700 people are still missing in Kosovo.
Jahjaga's office said the president had discussed with Moore the need for "an independent judicial process to close this difficult chapter in Kosovo's history".
A Western official close to the investigation told Reuters: "This is not about re-writing history or condemning any specific movement."
(Reporting by Fatos Bytyci; Editing by Matt Robinson and Andrew Heavens)