The Specialist Chamber was set up in The Hague in 2015 to handle cases of alleged crimes by Kosovo Liberation Army (KLA) guerrillas during the war that led to Kosovo’s independence from Serbia a decade later.
The indictment is "the result of a lengthy investigation and reflects the SPO's (Special Prosecutor's Office) determination that it can prove all of the charges beyond a reasonable doubt," the SPO said in a statement.
It said "others" had also been indicted including Kadri Veseli, a former speaker of Kosovo's parliament. Thaci and Veseli, both ex-top commanders in the KLA, have previously denied involvement in any war crimes during the late 1990s conflict. The SPO gave no details of the alleged war crimes.
It also said Thaci and Veseli were believed "to have carried out a secret campaign to overturn the law that created the Court and otherwise obstruct the work of the Court in an attempt to ensure that they do not face justice."
There was no immediate reaction from Thaci. But his office said later on Wednesday he had canceled a trip to the White House in Washington for a planned first round of US-mediated talks with Serbia on normalizing relations - among conditions the European Union has set for either country to join the bloc.
The Specialist Chamber is governed by Kosovo law but is staffed by international judges and prosecutors.
War crimes allegations against the KLA first surfaced in a 2011 report by the Council of Europe rights agency that accused guerrillas of killing civilian Serbs and ethnic Albanian political opponents during the 1998-99 conflict.
Local efforts to investigate alleged KLA war crimes have so far been foiled by widespread intimidation in the tiny state where clan loyalties run deep and former rebels are lionized.The special prosecutor's office is based in the Netherlands partly to help ensure protection of witnesses.