Kosovo leader Hashim Thaci has met with prosecutors in The Hague after they indicted him last month for alleged war crimes and crimes against humanity during Kosovo's 1998-99 uprising against Serbian rule.

Before entering the Specialist Chamber, set up in 2015 to handle cases of war crimes, Thaci told reporters he stood for "truth, reconciliation and peace."

Thaci had earlier accepted an invitation by the court to discuss the allegations against him and was expected to fly back home later in the day after the meeting. He has previously denied involvement in any war crimes during the conflict.

"Today I am here to respect what I dreamt and fought for – a free, independent Kosovo based on equal rights, multi-ethnic society and rule of law," Thaci told reporters outside the Kosovo Specialist Chambers.

"I am ready to face the new challenge and succeed for my son, my family, my people and my country. Nobody can rewrite history. This is a price of freedom."

The indictment, which also covers alleged crimes against humanity, is not final and a judge will now take several months to decide whether the case built by the special prosecutor's office is strong enough to put him on trial.

Prosecutors hold Thaci, former top commander of the Kosovo Liberation Army (KLA), responsible for nearly 100 murders of civilians during the war.

Around 20 ethnic Albanians demonstrated outside the Chamber in support of Thaci, waving Kosovo and Albanian flags.

The Kosovo Specialist Chamber is governed by Kosovo law, but is staffed by international judges and prosecutors and is based in the Netherlands partly to help ensure protection of witnesses. 

The talks on Monday came the day after the European Union said talks between Serbia and Kosovo were "back on track."

Kosovo's second top official Avdullah Hoti and Serbia's President Aleksandar Vucic, took part in a video call on Sunday, which was mediated by EU foreign policy chief Josep Borrell. They are due to hold face-to-face talks later this week.

During his comments to reporters before the talks, Thaci also said: "Kosovo is a success story, I am very proud. I believe in peace through reconciliation and justice. I believe in dialogue and relations with all nations."