Secret NATO documents based on intelligence reports, which were leaked to the Guardian, indicated that the US and other western powers backing Kosovo's government have had extensive knowledge of its criminal connections for several years.
Marked 'USA KFOR', the papers provided detailed information about organized criminal networks in Kosovo, based on reports by western intelligence agencies and informants.
The geographical spread of Kosovo's criminal gangs is outlined, alongside details of alleged familial and business links.
The Council of Europe is this week debating claims that Thaci was the head of a 'mafia-like' network responsible for smuggling weapons, drugs and human organs during and after the 1998-99 Kosovo war.
The organ trafficking allegations were contained in an official inquiry published last month by the human rights rapporteur Dick Marty.
His report accused Thaci and several other senior figures who operated in the Kosovo Liberation Army (KLA) of links to organized crime.
The report also named Thaci as having exerted 'violent control' over the heroin trade, and appeared to confirm concerns that after the conflict with Serbia ended, his inner circle oversaw a gang that murdered Serb captives to sell their kidneys on the black market.
Kosovo functioned as a UN protectorate from the end of the Kosovo war until 2008, when it formally declared independence from Serbia.
Thaci, who was re-elected prime minister last month, has been strongly backed by NATO powers. His government has dismissed the Marty report as part of a Serbian and Russian conspiracy to destabilize Kosovo.