Kosovo president and former guerilla leader Hashim Thaci was in detention in The Hague on Thursday, just hours after he resigned to face an indictment at a war crimes court.

The 52-year-old announced he was stepping down to "protect the integrity" of the presidency after a judge confirmed an indictment against him linked to the 1990s conflict with Serbia, when Thaci was political chief of the rebel Kosovo Liberation Army.

"I will cooperate closely with justice. I believe in truth, reconciliation and the future of our country and society," he told a press conference in Pristina, before leaving on a military aircraft for the Netherlands.

The indictment charges Thaci and three other suspects who are also in detention with war crimes and crimes against humanity, including murder, torture, illegal detention, enforced disappearances and persecution, the court said.

They were "transferred to the detention facilities of the Kosovo Specialist Chambers" in the Dutch city and will make their first appearances before the tribunal at a later date, it said.

A former premier who became president in 2016, Thaci has long stressed his innocence in a war that most Kosovars consider a just liberation struggle against Serbian oppression.

Kosovo's majority ethnic Albanian population suffered heavily during the 1998-99 separatist conflict, which claimed 13,000 lives and ended only after a NATO bombing campaign 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 in Kosovo -- have also been accused of revenge attacks on Serbs, Roma and ethnic Albanian rivals during and after the war.

Kosovo President Hashim Thaci has long insisted on his innocence
Kosovo President Hashim Thaci has long insisted on his innocence AFP / STRINGER

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.

Since then suspense has run high over if and when a pre-trial judge would confirm the indictment.

The Hague court said the three other suspects were transferred to its detention centre on Wednesday and Thursday. These are former rebel spokesman Jakup Krasnigi, Thaci's closest political ally Kadri Veseli, and key Kosovo Liberation Army figure Rexhep Selimi.

EU police arrested Krasnigi in Pristina on Wednesday

The Kosovo court was set up with EU backing five years ago, following a 2011 Council of Europe report which named Thaci and others as allegedly being involved in crimes.

The court operates under Kosovo law but is based in the Netherlands to protect witnesses from intimidation in a society where former rebel commanders remain hugely influential.

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

Known for his shrewd political manoeuvres and by the nom de guerre "Snake", Thaci is far from a hero to all at home.

Critics see him as the face of an entrenched political elite whose corruption and mismanagement have mired ordinary Kosovars in grinding poverty and warped its young democratic institutions.

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.

In Thaci's absence, parliamentary speaker Vjosa Osmani will serve as acting president.