Kosovo President Hashim Thaci has resigned from office, announcing that a special court at The Hague is indicting him for war crimes.

Earlier this year a special prosecutor accused him and others of being “criminally responsible” for 100 murders, during Kosovo’s 1998-99 independence war against Serbia.

Mr Thaci denies any wrongdoing.

There was no immediate confirmation from the Hague but later reports said he had left for The Hague on a plane.

A former senior commander of the Kosovo Liberation Army (KLA), he later turned to politics, in common with a number of KLA colleagues.

Two other former KLA officials were also on the plane, the Koha Ditore website reported: Kadrim Veseli, leader of the Democratic Party of Kosovo, and Rexhep Selimi, a Kosovo MP. Mr Veseli said he was travelling voluntarily to face “unjust accusations”.

Former KLA spokesman Jakup Krasniqi, 69, who later became president of Kosovo, was arrested on Thursday night by police working for the EU mission in Kosovo and taken to the Hague earlier. He faces charges of war crimes and crimes against humanity.

Mr Thaci said he was stepping down to ensure he would not face trial while serving as president. He said his resignation would “defend the integrity of the state”, and he called on people to remain calm.

His indictment had been expected since the special prosecutor made accusations in June that the Kosovo leader was “criminally responsible for nearly 100 murders”, torture and enforced disappearances.

The Kosovo Specialist Chambers (KSC) was set up in 2015 to investigate alleged crimes against ethnic minorities and political opponents by the KLA during the war in which Kosovo broke away from Serbia. The tribunal operates under Kosovo law but is staffed by international judges and prosecutors.

A 2011 Council of Europe report named Mr Thaci as the leader of a criminal offshoot of the KLA Kosovo Liberation Army. At the time he condemned the allegations as baseless. He spent several days with prosecutors in The Hague in July and made it clear at the time that he would stand down if he faced trial.

Serbia has already put on trial a number of former soldiers, paramilitaries and police for the killing of ethnic Albanians during the conflict at the end of the 1990s.