Kosovo President Hashim Thaci resigned Thursday to face an indictment from a war crimes court in The Hague, a dramatic downfall for a man who has loomed over the former Serbian province for more than a decade. 

The 52-year-old said he would step down to "protect the integrity" of the presidency after the court confirmed an indictment against him dating back to the 1990s conflict with Serbia, when Thaci was political chief of Kosovo's rebel army. 

"I will cooperate closely with justice. I believe in truth, reconciliation and the future of our country and society," he said at a press conference in the capital Pristina. 

Thaci, a former premier who has been president since 2016, has long insisted on his innocence over a war that many Kosovars consider a "just" struggle for their independence from Serbian oppression.

Kosovo's majority ethnic Albanian population suffered heavily during the conflict that claimed 13,000 lives and ended only after a NATO bombing forced Serb troops to withdraw from the province.

Serbian military and police officials were later convicted by international justice of war crimes.

But rebel leaders of the Kosovo Liberation Army (KLA)-- many of whom have gone on to dominate politics -- have also been accused of revenge attacks on Serbs, Roma and ethnic Albanian rivals during and after the war.

'100 murders' 

In June, prosecutors from the Hague-based Kosovo Specialist Chambers (KSC) accused Thaci and others of being "criminally responsible for nearly 100 murders" in addition to other crimes including enforced disappearance of people, persecution, and torture.

Thaci did not say Thursday which specific charges in the indictment had been confirmed.

Prosecutors declined an AFP request for comment. 

The president's closest political ally, Kadri Veseli, also said Thursday an indictment against him had been confirmed by the court and that he would go to The Hague.

Set up with EU-backing five years ago, the KSC operates under Kosovo law but is based in the Netherlands to protect witnesses from intimidation in a society where former rebel commanders are hugely influential. 

Prosecutors have twice accused Thaci of trying to undermine the work of the tribunal.

At home, Thaci is not a hero to all. 

For critics, he has become the face of a political elite whose corruption and mismanagement have done little to lift ordinary Kosovars out of grinding poverty. 

But few Kosovo Albanians will criticise the legacy of the KLA, with voices from across the political spectrum defending the war after Thaci was first accused. 

Twenty years later, relations between Kosovo and Serbia are still tense and complicated, with Belgrade refusing to recognise the independence Pristina declared in 2008.