Kosovo on Thursday awaited the return of President Hashim Thaci to respond to accusations of war crimes from the 1990s conflict with Serbia, as supporters and critics alike defended the "just" struggle that paved their path to independence.

Thaci was the former political leader of the ethnic Albanian guerilla group, the Kosovo Liberation Army (KLA), which launched a rebellion against Belgrade more than 20 years ago when Kosovo was a southern province of Serbia.

On Wednesday, he and others were accused a slew of war crimes and crimes against humanity linked to the 1998-99 war in an indictment filed by special prosecutors at the Kosovo Specialist Chambers in The Hague.

After the bombshell announcement, the president cancelled a planned trip to the US where he was set to discuss lingering tensions with Serbia.

Prosecutors accuse Kosovo President Hashim Thaci of trying to obstruct the work of the tribunal
Prosecutors accuse Kosovo President Hashim Thaci of trying to obstruct the work of the tribunal AFP / Armend NIMANI

His office had originally said he would return to Kosovo on Thursday but sources in Albanian said it was likely he would arrive in Pristina Friday. The presidency declined to comment.

The 52-year-old's only visible reaction was an update the cover photo of his Facebook profile to feature the crest of the KLA.

He has previously said he would comply with the court and that he is innocent and has "nothing to hide".

The indictment accuses Thaci and other suspects of murder, enforced disappearance, persecution and torture against "hundreds of known victims of Kosovo Albanian, Serb, Roma, and other ethnicities and include political opponents."

The charges still needs approval from a pre-trial judge but the prosecutors said they made the news public because Thaci and others have been trying to "obstruct the work" of the tribunal, which operates under Kosovo law but has international judges.

The Kosovo war cost about 13,000 lives
The Kosovo war cost about 13,000 lives AFP / JOEL ROBINE

It is unlikely that the 52-year-old would face arrest before the indictment is approved by a judge, which could take months, though a court spokesperson declined to specify.

Meanwhile at home, both Thaci's fans and his detractors came to the defence of the rebels who rose up against Belgrade in a war that cost about 13,000 lives, overwhelmingly Kosovo Albanians.

Calling for calm and noting that all are innocent until proven guilty, the government underlined that the war itself was "just and liberating and, as such, will remain one of the most important periods in the country's history".

In the capital Pristina, pensioner Qazim Fazlia said he found the court "unfair" for only investigating KLA fighters.

Timeline of the Balkans wars
Timeline of the Balkans wars AFP / Cecilia SANCHEZ

"We know that Serbia is the one that has committed crimes in Kosovo," he told AFP.

The left-wing party Vetevendosje, which is sharply critical of Thaci, also affirmed its belief "in the pure and just war of the KLA and we are committed now and always to defend it."

The conflict ended after a US-led NATO intervention in 1999 forced Serb troops to withdraw from the former province.

Top Serbian military and police officials were later convicted by international justice of war crimes during the conflict in which thousands of ethnic Albanian civilians were killed, tortured or forced to leave home.

But the KLA is also accused of atrocities against Serbs, Roma and ethnic Albanian rivals during and after the war.

Many rebel commanders have gone on to dominate Kosovo politically during its first decade of independence, which Serbia still rejects.

First as prime minister and now president, Thaci himself has remained at the centre of the political scene throughout.

Critics see him as the face of a entrenched political elite accused of rampant corruption and state capture.

His right-hand man Kadri Veseli, the KLA's former spy chief who now leads the political party founded by Thaci, was also accused of the crimes and has rejected them as "untrue".

Former prime minister Ramush Haradinaj, another ex-rebel, came to their defence.

"The Kosovo Liberation Army has waged a pure war, which resulted in the freedom and establishment of the Republic of Kosovo," he wrote on Facebook.

"We believe in the innocence of president Thaci, (party) president Veseli and all other comrades," he added.