Kosovo’s ex—prime minister Ramush Haradinaj must be retried on murder and torture charges related to the 1998—99 conflict, the Yugoslav war crimes tribunal said on Wednesday, calling his acquittal two years ago a miscarriage of justice.

The original trial for Haradinaj and two former Kosovo Liberation Army comrades was marred by intimidation that left two prosecution witnesses too scared to testify, tribunal President Patrick Robinson said.

“The trial chamber failed to appreciate the gravity of the threat that witness intimidation posted to the trial’s integrity,” Mr. Robinson said in handing down his decision.

Haradinaj had been accused along with Idriz Balaj and Lahi Brahimaj of abusing Serbs or their supporters in 1998 as Kosovo battled for independence from Serbia, which it eventually declared in 2008.

A date for the retrial has yet to be set, and it is unclear if the witnesses would testify in new hearings. Haradinaj showed no emotion in court on Wednesday at Mr. Robinson’s ruling, and was taken into custody along with Brahimaj. Balaj was not present in court.

“Given the potential importance of these witnesses to the prosecution’s case, the error undermined the fairness of the proceedings and resulted in a miscarriage of justice,” Mr. Robinson said.

Judges originally threw out all charges against Haradinaj and Balaj for lack of evidence, but convicted Brahimaj on charges of torture and sentenced him to six years.

Mr. Robinson ordered Haradinaj, Balaj and Brahimaj retried on six counts of the original indictment alleging murder, cruel treatment and torture of prisoners at a KLA headquarters and prison in the town of Jablanica. The appeals judges also upheld Brahimaj’s six—year sentence.

Haradinaj’s lawyer Michael O’Reilly said he was “extremely surprised” by the decision.

“It is something we could not have foreseen, particularly in view of his unambiguous acquittal two years ago,” Mr. O’Reilly said in a statement sent to The Associated Press. “Our concerns now are, first, to ensure Mr. Haradinaj’s quick return to Kosovo and, second, to get the earliest possible date for the partial retrial.”

Serbia’s deputy war crimes prosecutor Bruno Vekaric hailed the court decision as a “big victory of the Chief Prosecutor Serge Brammertz and his team in their struggle for the rights of the victims.”

Belgrade often accuses the court of bias because the vast majority of its suspects are Serbs.

Haradinaj was working in western Europe as a nightclub bouncer and construction worker when he returned to Kosovo to fight for its independence in the 1998—99 uprising against Serbia, and rose to become one of the most prominent rebel commanders.

He was a Western ally who harboured NATO special forces as they chose targets for airstrikes in 1999 as the Alliance bombed Serbia to end its crackdown on the separatists.

Afterwards, he was seen as a political leader prepared to bridge the divide between ethnic Albanians and Kosovo’s Serb minority. He formed the Alliance for the Future of Kosovo, known as AAK political party, and was elected prime minister in December 2004.

But he lasted just 100 days in office before quitting in March 2005 after learning of the indictment against him and surrendering to authorities in The Hague.

Haradinaj returned to head the opposition AAK after his acquittal, but the party has struggled to regain the support it enjoyed during his time as Kosovo’s prime minister.

Wednesday’s decision came a day before the U.N.’s highest judicial organ, the International Court of Justice, is expected to issue a nonbinding advisory opinion on the legality of Kosovo’s 2008 declaration of independence.

The retrial comes as the war crimes tribunal is under pressure from the Security Council to wrap up its final cases and shut its doors for good.

The court has finished the cases against 129 of the 161 suspects indicted by prosecutors. Two suspects remain on the run, former Bosnian Serb military chief Gen. Ratko Mladic and Goran Hadzic, a former leader of Croatian Serbs.

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