The document also says that the U.S. and other Western nations were aware of Thaci's alleged crimes but still backed his rise to power
The report is the culmination of a two-year investigation by Swiss senator and former prosecutor Dick Marty, who interviewed numerous witnesses too terrified to publicly testify against political figures and former members of the Kosovo Liberation Army (KLA), and analyzed secret reports from the FBI and other intelligence sources.
Marty writes that at the end of 1998-99 Kosovo war, Thaci was described by NATO intelligence sources as "the most dangerous of the KLA's 'criminal bosses.'" He is accused of heading a small but powerful criminal network, known as the Drenica Group, that allegedly began organizing illegal rackets in the buildup to the war.
One alleged money-making scheme involved smuggling a "handful" of captive Serbs, and some ethnic Kosovan Albanians, into neighboring Albania in the months after the war, where their organs were harvested.
"The testimonies on which we based our findings spoke credibly and consistently of a methodology by which all of the captives were killed," the report states, "usually by a gunshot to the head, before being operated on to remove one or more of their organs." The document does not personally implicate Thaci -- who served as the KLA's political head during the war -- in these killings.
The murders were carried out on a converted farmstead in the town of Fushë-Krujë, some 12 miles north of the Albanian capital Tirana, which had been turned into "a state-of-the-art reception center for the organized crime of organ trafficking."
The scene inside the clinic is detailed in the paper. "At least some of these captives became aware of the ultimate fate that awaited them," it states. "In detention facilities where they were held in earshot of other trafficked persons, and in the course of being transported, some of these captives are said to have pleaded with their captors to be spared the fate of being 'chopped into pieces.'"
After extraction, victims' kidneys were flown out of the country and sold on the black market. According to a separate investigation by The Guardian, some of those organs were shipped to Istanbul, as part of a criminal scheme operated by Turkish doctor Yusuf Sonmez.
Interpol is now attempting to hunt down the fugitive doctor for his part in an organ trafficking racket discovered by police in 2008. That scam saw impoverished Russians, Moldovans and Turks lured to the Medicus Clinic in Pristina with the false promise of payments for their kidneys. The donors received nothing, but their organs were sold for up to $200,000 to patients in Canada, Germany and Israel.
The Council of Europe report says that the removal of organs from captives in Albania a decade ago is "closely related to the contemporary case of the Medicus clinic." It cites "Kosovan Albanian and international figures" who were key "co-conspirators" in both crimes.
Their names have been omitted from the report "out of respect" to Kosovo's judicial process. However, The Guardian reports that sources within the Kosovan government say those unnamed individuals are Dr. Sonmez and former KLA medical commander Shaip Muja, who now advises Prime Minister Thaci on health policy.
The paper alleges that the two men became friends during the Kosovo war, and that Muja helped found the Medicus clinic.
Authorities have not accused Muja of any wrongdoing at Medicus, and he has denied being a member of the Drenica Group.
The Council of Europe paper doesn't comment on Muja's alleged connection to the clinic but states that it has uncovered "numerous convergent indications" of his decadelong involvement in "far less laudable international networks, comprising human traffickers, brokers of illicit surgical procedures and other perpetrators of organized crime."
The crimes outlined in Marty's report mostly took place in the chaotic months following the end of the Kosovo conflict, as international peacekeepers tried to restore law and order in the Serbian-ruled province.
NATO intervened in Kosovo in 1999 to stop a campaign of ethnic cleansing by Serb forces, who are believed to have butchered up to 10,000 ethnic Albanian civilians in just under two years. After 11 weeks of bombing raids by Western air forces, Serbian strongman Slobodan Milosevic pulled his troops out of the province, which declared independence in 2008.
Although the international community strongly condemned Serbian atrocities, Marty writes that the West opted to ignore suspected KLA war crimes, "placing a premium instead on achieving some degree of short-term stability."
He notes that witnesses "credibly implicated" Thaci and four other members of the Drenica Group "in having ordered -- and in some cases personally overseen -- assassinations, detentions, beatings and interrogations in various parts of Kosovo" and Albania from 1998 to 2000.
The same five ex-KLA commanders have held key positions in the country's government over the past decade and secured the support of Western powers keen to prevent further violence. But as well as holding important political positions, the document states that the men have also continued to be major players in the region's crime syndicates.
"In confidential reports spanning more than a decade, agencies dedicated to combating drug smuggling in at least five countries have named [Thaci] and other members of his 'Drenica Group' as having exerted violent control over the trade in heroin and other narcotics," Marty writes.
He adds that he studied these international intelligence reports "with consternation and a sense of moral outrage" as officials in the U.S. and Europe must "undoubtedly possess the same, overwhelming documentation of the full extent of the Drenica Group's crimes, but none seems prepared to react in the face of such a situation and to hold the perpetrators to account."
The European Union, which has some 2,000 police and justice workers in Kosovo, today declared that it was prepared to look into the allegations contained in Marty's report.
"We take allegations on war crimes and organized crime extremely seriously," said Maja Kocijancic, spokeswoman for EU foreign policy chief Catherine Ashton. "We have seen the report, and if the rapporteur, Mr. Marty, has any concrete evidence, we invite him to bring this forward to the relevant authorities," including the EU's police and justice mission in Kosovo, EULEX. That body handles cases that are too sensitive for the local judiciary, such as allegations of war crimes.
"[The report] is based on groundless facts which are invented with a goal to harm Kosovo's image," it said in a statement issued Tuesday. The party added that it would "take all possible and necessary steps in order to confront Marty's fabrications, including legal and lawful ones," it warned.
The Serbian government, which refuses to recognize Kosovo's 2008 declaration of independence from Serbia, questioned whether Thaci could hold on as prime minister. "I do not know what future that person has, if one takes into account the Council of Europe report," said Serbian Foreign Minister Vuk Jeremic.