The president of Kosovo has been accused of involvement in almost 100 murders and other war crimes including torture and “enforced” disappearances.

The Office of the Special Prosecutor (SPO) in the Hague filed an indictment to charge 10 people including President Hashim Thaci and Democratic Party leader Kadri Veseli, with “crimes against humanity”.

In a statement released Thursday morning (Australian time), prosecutors said they were making the names public in a bid to combat Mr Thaci and Mr Veseli’s “repeated efforts…to obstruct and undermine” the work of the Kosovo Specialist Chambers.

“Mr Thaci and Mr Veseli are believed to have carried out a secret campaign to overturn the law creating the court and otherwise obstruct the work of the court in an attempt to ensure that they do not face justice,” the SPO said.

“By taking these actions, Mr Thaci and Mr Veseli have put their personal interests ahead of the victims of their crimes, the rule of law, and all people of Kosovo.”

The indictment was the first by the special tribunal based in the Hague, and is part of an investigation into crimes against ethnic Serbs during and after Kosovo’s 1998-99 independence war with Serbia.

The 1998-1999 war left more than 10,000 dead. Another 1641 are still unaccounted for – and investigators believe Mr Thaci and the other accused men were involved in the “enforced” disappearances.

Kosovar refugees queue in a long line expecting food handout, at a NATO-run refugee camp in Stenkovec, on the outskirts of Skopje, in April 1999. Photo: AAP

Other charges against the leaders include persecution and torture.

The indictment is “the result of a lengthy investigation”, the SPO said,  and prosecutors are confident they “can prove all of the charges beyond a reasonable doubt”.

“The Indictment alleges that Hashim Thaci, Kadri Veseli, and the other charged suspects are criminally responsible for nearly 100 murders,” the SPO said.

“The crimes alleged in the Indictment involve hundreds of known victims of Kosovo Albanian, Serb, Roma, and other ethnicities and include political opponents.”

Mr Thaci commanded fighters in the Kosovo Liberation Army, or KLA, during the war.

The Indictment is the result of a lengthy investigation and reflects the SPO’s determination that it can prove all of the charges beyond a reasonable doubt. Photo: AAP

Mr Veseli, a former parliament speaker and leader of the opposition, was formerly a chief of the Kosovo Intelligence Service.

The court has been operating since 2015 and has so far questioned hundreds of witnesses.

Kosovo’s prime minister resigned last year before he was questioned.

The indictment is being reviewed by a pre-trial judge who will decide whether to confirm the charges, according to the statement.

-with AAP