Kosovo's leader Hashim Thaci resigned on Thursday in order to face charges for war crimes and crimes against humanity at a special court based in The Hague.

After announcing his resignation at a news conference in Pristina, Kosovo, Thaci said he was taking the step "to protect the integrity of the presidency of Kosovo."

Thaci was indicted by the court in the Netherlands, which was set up to try the alleged crimes of former ethnic Albanian rebel leaders.

"I will cooperate closely with justice. I believe in truth, reconciliation and the future of our country and society," Thaci, who denies wrongdoing, said at the press conference in the country's capital.

Thaci is one of several politicians who have been indicted for crimes including murder, enforced disappearances, persecution and torture. Among them is also a former parliament speaker, Kadri Veseli.

Three other former commanders of the Kosovo Liberation Army (KLA), which fought for independence from Serbia, have been charged with war crimes by the court and an associated Special Prosecutor's Office established five years ago.

Exact details of the 10-count indictment against Thaci, Veseli and others have not been released. Announcing the existence of the indictment earlier this year, the Specialist Prosecutor's Office alleged that Thaci and others were "criminally responsible for nearly 100 murders."

The formation of the court and prosecutor's office followed a 2011 report by the Council of Europe, a human rights body, which included allegations that KLA fighters trafficked human organs taken from prisoners and killed Serbs and fellow ethnic Albanians.

The court is mandated to investigate and prosecute allegations of war crimes and crimes against humanity in Kosovo, or linked to the Kosovo conflict, from 1998 to 2000.

The 1998-1999 war for independence from Serbia ended after a 78-day NATO air campaign against Serbian troops.

In 2008, Kosovo declared its independence from Serbia, something that has divided global opinion – with Serbia and other countries across the world not recognizing this status.