Detained former Kosovo president Hashim Thaci will make his first appearance at a war crimes court in The Hague on Monday, the tribunal said.

Thaci resigned as president on Thursday to face charges over the 1990s conflict with Serbia, when he was political chief of the rebel Kosovo Liberation Army.

The one-time guerilla leader flew to the Netherlands shortly afterwards and was then placed in the detention centre of the Kosovo Specialist Chambers.

"The initial appearance of Hashim Thaci will take place in the courtroom" on Monday at 1400 GMT, in a public hearing, the court said in a statement on Friday.

A judge will ensure "that the rights of the accused, including the right to legal representation, are respected, and that the accused understands the charges."

Ex-Kosovo president Hashim Thaci will face a court on Monday over charges over the 1990s conflict with Serbia
Ex-Kosovo president Hashim Thaci will face a court on Monday over charges over the 1990s conflict with Serbia AFP / Armend NIMANI

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.

Thaci said in Pristina on Thursday he was stepping down to "protect the integrity" of the Kosovo presidency, adding that "I believe in truth, reconciliation and the future of our country and society."

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 Serbian troops to withdraw from the province.

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

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.