THE HAGUE, Netherlands (AP) — The International Criminal Court acquitted a Congolese militia leader Tuesday of all charges of commanding fighters who destroyed a village in eastern Congo in 2003, raping and hacking to death some 200 people, including children.

The acquittal of Mathieu Ngudjolo on charges including rape, murder and pillage was only the second verdict in the court’s 10-year history and the first time it had cleared a suspect.

The only other ICC verdict, handed down earlier this year, convicted another Congolese rebel leader, Thomas Lubanga, of using child soldiers in battles in Ituri. He was sentenced to 14 years in prison.

The court has indicted far more senior suspects than Ngudjolo, including Sudanese President Omar al-Bashir and former Ivory Coast president Laurent Gbagbo. Al-Bashir refuses to surrender to the court and Gbagbo is in custody in The Hague awaiting a possible trial.

The Tuesday’s verdict also cast a shadow over ICC prosecutors’ efforts to collect and present evidence of atrocities in complex conflicts thousands of miles from the court’s headquarters in The Hague.

Judges said the testimony of three key prosecution witnesses was unreliable and could not prove definitively that Ngudjolo led the rebel attack on the village of Bogoro, but they emphasized that Ngudjolo’s acquittal did not mean that no crimes occurred in the village.

“If an allegation has not been proven beyond a reasonable doubt … this does not necessarily mean that the alleged fact did not occur,” Presiding Judge Bruno Cotte of France said.

Eric Witte, an expert in international law at the Open Society Justice Initiative, said the judgment “will send a worrying signal about the quality of ICC prosecutions.”

He said Prosecutor Fatou Bensouda may now need to rethink the way her office builds its cases.

“A pattern of prosecution failures could undermine support for the court as a whole,” Witte warned.

Prosecutors say many villagers in Bogoro were raped before some 200 were hacked to death with machetes by rebel fighters on a single day in February 2003.

Rights organizations immediately called upon the court to explain the acquittal to victims and survivors in the village in Congo’s eastern Ituri region, and to improve its investigations.

“The acquittal of Ngudjolo leaves the victims of Bogoro and other massacres by his forces without justice for their suffering,” said Géraldine Mattioli-Zeltner, international justice advocacy director at Human Rights Watch. “The ICC prosecutor needs to strengthen its investigations of those responsible for grave crimes in Ituri, including high-ranking officials in Congo, Rwanda and Uganda who supported the armed groups fighting there.”

Judges ordered Ngudjolo’s immediate release, but Bensouda said she would appeal the acquittals and asked for Ngudjolo to be kept in custody.

Prosecutors argued that their appeal had a strong chance of success and that Ngudjolo could disappear if released and not return for the appeals case where his acquittal could be overturned.

“You have erred in fact and law,” prosecution lawyer Eric MacDonald told the judges, who said they would issue a decision later Tuesday on whether to release Ngudjolo.

Ngudjolo showed no emotion as Cotte acquitted him.

Judges are still considering the evidence against another militia leader, Germain Katanga, who stood trial with Ngudjolo, and are expected to deliver that verdict next year.

Ngudjolo’s lawyer, Jean-Pierre Kilenda, said his client had always insisted he was innocent.

Judges “showed that this court respects the rights of defendants,” the lawyer said.

Congo faces a myriad of rebel groups including the emergence of one known as M23, sparking fighting that has forced hundreds of thousands to flee their homes in the country’s volatile east.

Kambasu Ngeve, M23′s chief negotiator in ongoing talks with the Congolese government, said he was delighted by Tuesday’s acquittal.

“I still thought that all those were brought to the ICC in the Ituri case were innocent and that the real culprits were free,” he told The Associated Press. “It doesn’t surprise me. I only regret that he spent a long time in prison.”

Congolese government spokesman Lambert Mende said only that “the government takes note of this decision, which we cannot interpret because it’s a judicial order and justice is independent.”

The ICC, the world’s first permanent war crimes tribunal, was set up by the Rome Statute treaty that came into force in 2002 and has been ratified by 121 nations. Prosecutors have so far indicted suspects in seven different countries, all of them in Africa including Congo, Sudan, Kenya, Libya and Ivory Coast.

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Associated Press writer Saleh Mwanamilongo in Kinshasa, Congo, contributed to this report.

Copyright 2012 The Associated Press.