(CNN) -- The authorities who control Kosovo may have stolen organs from prisoners of war and political rivals when the Kosovo Liberation Army was fighting Serbian forces for control of the territory, European authorities allege in a new report.
"Numerous indications seem to confirm that ... organs were removed from some prisoners ... to be taken abroad for transplantation," according to a draft report from the Council of Europe.
Investigators have "made progress" toward "proving the existence of secret KLA places of detention in northern Albania where inhuman treatment and even murders are said to have been committed," draft author Dick Marty says.
Illegal organ trafficking continued after the war ended, the draft suggests.
Nearly 1,900 people who disappeared during the conflict still have not been found, and another 500 disappeared after NATO troops arrived in June 1999, Marty says.
And links between "criminal activity" and "certain KLA militia leaders ... has continued, albeit in other forms, until today," he report charges.
Prime Minister Hashim Thaci of Kosovo is one of the founders of the Kosovo Liberation Army. The report names him as the "boss" of a prominent faction in the militia that "apparently wrested control" of "illicit criminal enterprises" from rivals across the border in Albania.
His office refused to comment on the allegations.
Kosovo's government called the report "defamatory" and "mendacious," saying the allegations "have been constructed to damage the image of Kosovo and the Kosovo Liberation Army."
Kosovo's acting President Jakup Krasniqi -- a Thaci ally -- expressed deep indignation about the report, saying it was "nothing but fabricated and irresponsible statements."
Albanian Prime Minister Sali Berisha said it was "based on no facts, evidence or reality. Thus it proves political line of the author, who flagrantly abuses the authority of the Council of Europe."
European Union officials in Kosovo said that anyone with concrete evidence of war crimes or organized crime should come forward.
"The mission is already investigating and prosecuting a number of cases related to war crimes and organized crimes," spokesman Blerim Krasniqi said.
On Thursday, the report will be debated by a committee of the Council of Europe, an organization with 47 member countries that seeks to promote democracy and human rights. The council's parliament plans to debate it in January.
The report is based partially on investigations by European Union officials and was written by Dick Marty for the Council of Europe's Committee on Legal Affairs and Human Rights.
Investigators are not getting enough cooperation from either Albania or Kosovo, the report adds.
Kosovo's majority population is ethnic Albanian. Serbs are the minority.
The KLA was backed by NATO bombing when it fought for independence from Serbia in the late 1990s.
Kosovo has made it "complicated" to dig for missing bodies, and Albania has refused to allow it, Marty says, adding: "Serbia ultimately cooperated."
Russian Foreign Minister Sergey Lavrov said Wednesday, "We are very seriously concerned about the published information."
He was appearing in a joint news conference in Moscow with Serbian Foreign Minister Vuk Jeremic.
The report from the Council of Europe -- which is separate from the European Union -- was prompted partly by allegations made in a book in 2008.
Carla Del Ponte, the former chief prosecutor of the International Criminal Court for the former Yugoslavia, leveled the accusation in her memoir "Madame Prosecutor."
The court opened an investigation into the allegations but dropped it, the Council of Europe said, without explaining why. Evidence has since been destroyed, Marty's draft says.
He acknowledges the chaotic situation in Kosovo after the war but also criticizes the international community for tending to see Serbs as aggressors and Kosovars as victims.
"The reality is less clear-cut and more complex," Marty writes.
But the international authorities who took control after the 1999 war felt that they "needed to promote short-term stability at any price, thereby sacrificing some important principles of justice."
Kosovo was a province of Serbia but declared independence in 2008. About 70 countries have recognized the declaration, but Serbia does not, and international organizations including the United Nations and European Union continue to have administrators in Kosovo.
Journalist Vlora Rustemi in Pristina, Kosovo, and CNN's Maxim Tkachenko in Moscow contributed to this report.