By DAN BILEFSKY and SOMINI SENGUPTAJULY 29, 2014

PARIS — A special European Union prosecutor said Tuesday that senior members of the Kosovo Liberation Army engaged in a campaign of persecution against ethnic Serbs after the 1998-99 Kosovo war, and said evidence suggested that the armed group had targeted a number of individuals after the war to harvest and sell their organs.

Kosovo declared independence from Serbia on Feb. 17, 2008, almost a decade after NATO bombs helped eject the former Serb strongman Slobodan Milosevic from Kosovo, ending a brutal civil war against the ethnic Albanian majority. But regional reconciliation has been hampered by accusations that senior members of the Kosovo Liberation Army, known by its initials K.L.A., have not been held fully accountable for suspected war crimes.

A European Union task force was set up in September 2011 under the leadership of Clint Williamson, an American diplomat who served as the war crimes envoy in the administrations of George W. Bush and President Obama. The task force was created after a Council of Europe report accused Kosovo’s prime minister, Hashim Thaci, the former commander of the K.L.A. of having led a “mafialike” group that smuggled human organs, weapons and heroin during and after the war. Mr. Thaci has strenuously rejected those accusations and the Kosovo government at the time called them “despicable.”

While refusing to describe whether Kosovo’s current political leadership was potentially implicated in war crimes, Mr. Williamson said at a news conference on Tuesday in Brussels that the suspects included “individuals at the most senior levels of the K.L.A.”

He said senior officials of the guerrilla group had intentionally targeted minority populations with acts of persecution that included “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.”

Mr. Williamson added that the practice of removing organs for transplant had occurred on a limited scale and that evidence suggested that a “handful” of individuals were killed for the purpose of extracting and trafficking their organs. But he said there was currently insufficient evidence to prosecute anyone for the crimes, adding that the investigation had been tainted by witness intimidation in Kosovo.

"If even one person was subjected to such practice that is a terrible tragedy,” he said, referring to the accusations of organ trafficking. “The fact that it occurred on a small scale does not lessen the savagery of the crime.”

He said the persecution resulted in the ethnic cleansing of minority Serb and Roma communities from parts of the country. It also targeted ethnic Albanians who were political enemies of K.L.A. leaders, he said.

Mr. Williamson’s statements are a blow to Kosovo, a poor country that has been struggling to find international legitimacy since it declared independence with the support of the United States and a majority of European Union countries. His conclusions will most likely be welcomed by Serbia, which has long argued that international justice has unfairly focused on Serbs suspected of war crimes at the expense of those who targeted Serbs during the war and its aftermath.

On Tuesday, the Kosovo government said it was determined to cooperate with the investigation. Petrit Selimi, the deputy foreign minister, said Mr. Williamson’s statements offered no new elements. “Kosovo’s war for liberty was a just cause supported by the free world, while individuals who may have allegedly engaged in unlawful behavior under the umbrella of a guerrilla army must face justice,” he said in an emailed statement.

The possible indictment of K.L.A. leaders comes more than a decade after the alleged war crimes occurred. There is no statute of limitations for war crimes under international law, a fact that has fueled several efforts to document crimes in Syria’s continuing war, including seven successive reports by a United Nations commission of inquiry.

Mr. Williamson said a special tribunal was expected to be established early next year, with the goal of trying alleged war crimes committed in the immediate aftermath of the Kosovo war. Crimes committed during the war have been tried in the International Criminal Tribunal for the former Yugoslavia, where Mr. Williamson was once a prosecutor.

The new court is likely to face challenges. Past investigations of reports of organ trafficking in Kosovo have been undermined by witnesses’ fears of testifying in a small country where clan ties run deep and former members of the K.L.A. are still feted as heroes.

Former leaders of the K.L.A. occupy high posts in the government, and the extent to which they will cooperate with investigations remains unclear.