The charges, which include murder, enforced disappearances, persecution and torture, were filed by special prosecutors investigating crimes from Kosovo’s uprising against Serbia two decades ago.
Thaci, 52, was the political leader of the ethnic Albanian rebels who waged the separatist conflict that paved the path for Kosovo’s independence.
“If the accusation is confirmed, I will immediately resign as your President and face the accusations,” Thaci, considered Kosovo’s most powerful politician, said in his first national address following the allegations.
“I will not face justice from this office,” he added.
The indictment still needs approval from a pre-trial judge, which could take months, to try the president.
But prosecutors said they rushed the announcement because Thaci and other suspects had been trying to obstruct the work of the Kosovo Specialist Chambers, a Hague-based court that operates under Kosovo law but has international judges.
The indictment accused Thaci, his closest political ally Kadri Veseli and others of being “criminally responsible for nearly 100 murders” in addition to other crimes against Serb, Roma and Kosovo Albanian victims.
In his speech Thaci insisted he was “not a saint” but that “there has not been, and could not be, even a single piece of evidence addressed to Hashim Thaci for violations of any law.”
US summit scrapped
President since 2016 and prime minister before that, Thaci has dominated Kosovo politically ever since he helped sever it from Belgrade.
That conflict ended after a NATO bombing forced Serb troops to withdraw from Kosovo in 1999.
Serbian military and police officials were later convicted by international justice of war crimes during the conflict that left 13,000 people dead, mainly ethnic Albanians.
But rebels from the Kosovo Liberation Army (KLA) have also been accused of coordinating a campaign of revenge attacks on Serbs, Roma and ethnic Albanian rivals during and after the war.
Like Thaci, many rebel commanders dropped their fatigues for politicians’ suits during Kosovo’s first decade of independence.
Critics accuse them of miring the young democracy in corruption while doing little to lift ordinary Kosovars from poverty.
But the war crimes charges have upset even Thaci’s detractors, who are steadfast in their support of Kosovo’s “just” independence struggle.
Twenty years later, Serbia still refuses to accept Kosovo’s statehood, a constant source of tension in the region.
Thaci was forced to cancel a trip to the US to discuss lingering hostilities with his Serbian counterpart after the charges were announced, scuppering the summit.