An EU prosecutor’s accusations of ethnic cleansing by Kosovo Liberation Army commanders reveal uncomfortable truths for the West.

An image has stayed with me from a hot summer day in Kosovo in 1999. The burned-out ruins of a house are smouldering beneath a blue sky. A British soldier is trying to douse them with a trickle of water from a garden hose.

It was a safe bet that the house in Pristina, like countless others across Kosovo set ablaze that summer, belonged to a Serb or someone from another ethnic minority. The scene seemed to sum up the inadequacy of NATO peacekeepers’ response to the ruthless violence of those hell-bent on forcing Serbs and others to flee or die.

As a journalist based in Kosovo for about a year from mid-1999, I wrote many stories about killings and kidnappings of Serbs, about rocket and grenade attacks and shootings that targeted them or other minorities. It was a depressing drip-drip of hatred.

We reporters initially wrote of “revenge attacks” – a neat way to convey that members of Kosovo’s ethnic Albanian majority were hitting back after suffering atrocities at the hands of Serb forces. It later seemed clear that some of this violence was far from spontaneous; it was organised, but to what extent and by whom remained murky.

Now, 15 years later, a European Union prosecutor has declared that he has evidence to prove that such attacks were not just individual acts of fury but something far more sinister — a campaign of ethnic cleansing organised by several top commanders of the Kosovo Liberation Army, the guerilla group that fought Serb forces in the late 1990s and helped draw NATO into the conflict.

The prosecutor, Clint Williamson, expects his office to file an indictment charging KLA leaders with crimes against humanity and war crimes. They will stand accused of unlawful killings, abductions, illegal detentions and sexual violence.

Williamson’s statement should prompt soul-searching not just in Kosovo but also at NATO, the United Nations and in Western capitals. If he is correct, an orchestrated campaign to wipe out minority communities took place when the UN was in charge of Kosovo and thousands of NATO troops were responsible for security.

In bombing Yugoslavia in 1999 to drive out Serb forces, NATO also acted as the KLA’s de facto air force. Yet Williamson concludes that in both 1998 and 1999, elements of the KLA were also conducting a campaign of violence and intimidation against Kosovo Albanian political opponents that included executions and abductions.

It will not be easy to dismiss Williamson’s conclusions. He has spent almost three years examining the case. He and his team have conducted hundreds of interviews and reviewed thousands of pages of documents.

Accusations that the prosecutor is biased against Kosovo Albanians will not wash. As he said last Tuesday, he supervised investigations into Serb war crimes in Kosovo, including the exhumation of mass graves where thousands of ethnic Albanians were buried. He co-wrote the indictment against Slobodan Milosevic for those crimes.

Williamson knows very well what Serb forces did to Kosovo Albanians. But he is also in no doubt about what happened afterwards — “a brutal attack on significant portions of the civilian population… directed against almost all of the Serbs who wanted to stay in Kosovo, many of whom were elderly and infirm”. The campaign extended to other minorities such as Roma, branded collaborators with the Serbs.

For Kosovo, which declared independence in 2008, this will have major political repercussions. Williamson has not named those who will be indicted but he said they were at the “senior-most levels” of the KLA. Several prominent Kosovo politicians fit that description. The possibility of an indictment and trial will hang over them for a considerable time. The special court needed to try the case has not even been set up yet – and won’t be until early next year at the very earliest.

But the implications for NATO, the UN and Western leaders past and present are also significant. The conditions they established in postwar Kosovo allowed too much “tolerance for intolerance”, in the memorable phrase of Dennis McNamara, the head of the UN refugee agency’s operations there at the time.

Western governments did not apply enough pressure on KLA leaders to end the violence. Peacekeepers were not tough enough in enforcing law and order. A credible justice system was not established. Just before ending his year in Kosovo, McNamara described the environment there as “pretty much a free-for-all for a long period”.

There was not much tolerance in official circles for McNamara’s views. Western governments and NATO leaders were keen to portray the Kosovo war as a great success — which it was, in one very important sense. Hundreds of thousands of ethnic Albanians were able to return to Kosovo, rebuild their homes and live free of Serb repression. But the failure to establish post-war order was hugely costly.

Not learning from this mess was costlier still. Kosovo should have taught Western governments that any country or coalition taking military action must fill the subsequent vacuum swiftly and firmly. Otherwise it will overflow with violence and lawlessness. The failure to learn that lesson reverberates today, in Afghanistan, in Libya and most catastrophically in Iraq.

Andrew Gray was a Reuters reporter in Pristina from June 1999 to October 2000, then Belgrade bureau chief and chief Balkans correspondent until 2004.