Leading political figures in Kosovo face indictment by a special EU court for crimes against humanity, including killings, abductions, sexual violence and other abuses of Serb and Roma minorities, according to the chief prosecutor leading a three-year special investigation (pdf).

The threat of indictments comes in a progress report published on Tuesday morning in Brussels by Clint Williamson, an American prosecutor appointed by the EU in 2011 to investigate ethnic cleansing committed in Kosovo since the 1999 Nato intervention brought an end to the conflict there.

Williamson does not name the suspects but describes them as "senior officials of the former Kosovo Liberation Army" (KLA), which fought an insurgency against the Serbian regime of Slobodan Milosevic. Many former KLA commanders went on to leadership positions after Kosovo declared independence in 2008. It is believed at least some of the indictments prepared by the EU special investigative task force (SITF) are against top figures still actively involved in politics.

Williamson's investigation confirmed earlier allegations that in a "handful" of cases, organs taken from executed prisoners were trafficked for profit, but 15 years after the crimes, the SITF has not been able to gather enough concrete evidence to mount a viable prosecution.

The indictments for wholesale human rights violations are likely to have a far-ranging impact on Kosovo's future and will be embarrassing for the US and western European governments, which provided enthusiastic backing for the KLA leadership during and after the war.

The indictments cannot be issued until a special court to try the cases is established, almost certainly in the Netherlands. But its creation has been held up by bureaucratic delays over funding in the European commission and political turmoil in Kosovo. Williamson said he hoped the court would be set up by early next year, but the cases will be tried by a new chief prosecutor. He will step down after a three-year term next month.

Williamson said he was leaving for personal reasons, to rejoin his family in the US, rather than professional factors.

"There have been press reports that I was leaving because the investigation is collapsing. That is completely untrue. I think we have had a very solid investigation with very good results," he told the Guardian.

In his report, Williamson said the investigation had been rendered far more difficult by pervasive intimidation of witnesses, describing it as "a dark cloud over the country".

"We have taken steps to counter the impact of the witness intimidation and we will continue to do so. We will actively investigate these activities and will prosecute any individuals found to have been involved," Williamson says in his report.

"There is probably no single thing that poses more of a threat to rule of law in Kosovo and of its progress toward a European future than this pervasive practice."

Ten thousand people died in the 1998-99 Kosovo conflict, many of them Kosovan civilians killed in a brutal Serbian counterinsurgency. War crimes committed by both Serbian forces and the KLA have been tried in the international criminal court for the former Yugoslavia (ICTY), but that did not examine abuses since 1999.

The EU investigation covered abuse of Kosovo Serbs and other minorities at the hands of the victorious KLA commanders.

The crimes include "unlawful killings, abductions, enforced disappearances, illegal detentions in camps in Kosovo and Albania, sexual violence, other forms of inhumane treatment, forced displacements of individuals from their homes and communities, and desecration and destruction of churches and other religious sites".

"This effectively resulted in the ethnic cleansing of large portions of the Serb and Roma populations from those areas in Kosovo south of the Ibar river, with the exception of a few scattered minority enclaves," the SITF report says.

"We believe that the evidence is compelling that these crimes were not the acts of rogue individuals acting on their own accord, but rather that they were conducted in an organised fashion and were sanctioned by certain individuals in the top levels of the KLA leadership. The widespread or systematic nature of these crimes in the period after the war ended in June 1999 justifies a prosecution for crimes against humanity."

The SITF investigation largely confirms the findings of an earlier Council of Europe enquiry led by a Swiss politician, Dick Marty, in 2010.

It upholds the Marty report's finding that a "handful" of prisoners had been murdered so that organs could be taken and sold. But Williamson said that "to prosecute such offences … it requires a level of evidence that we have not yet secured."

"Fifteen years down the line, we have solid information that these things happened, but no physical evidence. There are no bodies, no names of victims," Williamson told the Guardian.

"The likely reaction of a defence counsel in a murder case would be: there's not enough information to know what I am defending against, and a judge would probably agree. That said, it's certainly not beyond the realm of possibility that additional evidence will emerge in the next few months, and we will continue pursuing it."

The creation of a special European court would require a change in the Kosovo constitution and therefore a two-thirds majority in parliament. In theory, the suspects themselves could use their political power to obstruct it, but Williamson said that there would face substantial opposition inside Kosovo and beyond.

"I think it would be difficult for them politically if they attempted to block this. If the EU approach doesn't work, the most likely alternative is something set up through the UN security council and most Kosovars oppose that," Williamson said.

"So, it would be a hard sell to say that they were acting for the interests of Kosovo as opposed to just trying to save their own skins. There is a lot of pressure out there to make this work though and people across the political spectrum have been publicly supportive of it, so I am optimistic it will stay on track."