By Julia Fioretti
BRUSSELS, July 29 (Reuters) - An EU-led inquiry found "compelling indications" that Kosovo Albanian guerrillas extracted body organs from Serb captives during the 1998-99 war and sold them, but the practice was not widespread and there was not enough evidence for a trial, the lead investigator said on Tuesday.
After a three-year investigation, the EU-led task force said there was, however enough evidence to prosecute former leaders of the Kosovo Liberation Army (KLA) for war crimes against the ethnic Serb and Roma populations of Kosovo during the conflict.
The investigation was prompted by a 2011 report by Council of Europe member Dick Marty that accused senior KLA commanders of involvement in the smuggling of Serb prisoners into northern Albania and the removal of their organs for sale.
Prime Minister Hashim Thaci, himself a former KLA leader who was named in Marty's report, has dismissed the accusations as an attempt to tarnish the Kosovo Albanian fight for independence.
U.S. prosecutor John Clint Williamson, who led the investigation, said there was no evidence of widespread organ harvesting, but that the crime had occurred a number of times.
"There are compelling indications that this practice did occur on a very limited scale and that a small number of individuals were killed for the purpose of extracting and trafficking their organs," he told journalists.
Other crimes perpetrated by senior KLA members, such as unlawful killings and forced disappearances, amounted to the ethnic cleansing of large portions of the Serb and Roma populations, and there was enough evidence to prosecute, Williamson said.
The task force will file its indictment against former KLA leaders for war crimes once an ad hoc tribunal has been set up by the European Union and Kosovo, something Williamson said would happen next year. He did not name the people likely to be indicted.
Prime Minister Thaci said in a statement the government would continue cooperating with the task force.
"The government of the Republic of Kosovo appreciates the completion of the ambassador Williamson's work, which is an important step to determine potential individual responsibility and gives an end to the claims of the unfounded charges."
Serbia's counter-insurgency campaign of 1998 and 1999 eventually drew in NATO, which bombed for 78 days to drive out Serbian forces behind the killings of Kosovo Albanian civilians. Around 10,000 Albanians and just over 2,000 Serbs are believed to have been killed during and immediately after the war.
Kosovo declared independence in 2008 but the EU still plays a guiding role in policing and justice, particularly cases of war crimes.
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 former KLA rebels are revered as heroes.
Williamson condemned what he called "active efforts" to undermine the investigation.
"As long as a few powerful people continue to thwart investigations into their own criminality, the people of Kosovo as a whole pay the price as this leaves a dark cloud over the country."
(Additional reporting by Fatos Bytyci in Pristina; Editing by Robin Pomeroy)