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Jacques Mungwarere was found not guilty of crimes against humanity related to the 1994 Rwandan genocide, in an Ottawa courtroom Friday. The judge said Mungwarere was 'probably guilty,' but ruled the evidence was not clear enough to overcome reasonable doubt. (Sarah Wallace/CBC)

An Ontario Superior Court judge said Friday a Rwandan refugee accused of crimes against humanity is "probably guilty," but ruled the Crown didn't prove its case beyond all doubt.

Jacques Mungwarere, only the second person to be tried under the Crimes Against Humanity and War Crimes Act in Canada, would have faced an automatic sentence of life in prison with no chance of parole for 25 years if he had been convicted.

But the judge decided none of the witnesses on either side was completely believable — and therefore the threshold of guilt "beyond reasonable doubt" was not met.

The not guilty verdict, however, may not be the end of Mungwarere's legal troubles.

The Crown prosecutor says he has 30 days to appeal, and isn't ruling out that possibility.

Also, in the course of the trial, Mungwarere admitted to providing false information on his immigration papers when seeking asylum in Canada — a fact that could put his current refugee status at risk.

RCMP spent 6 years investigating

Mungwarere was living in Windsor, Ont., in 2003 when he was recognized by a man from his childhood.

That man immediately contacted the RCMP, saying Mungwarere wasn't an innocent refugee claimant but an active participant in the 1994 Rwandan genocide.

A special RCMP unit then spent six years investigating Mungwarere, making three trips to Rwanda to interview witnesses.

The Crown obtained a special order protecting the identities of many of the witnesses when it came to the trial.

Among attacks, rapes and murders, Mungwarere was accused of taking part in a massacre at a compound that included two churches and a hospital.

Hundreds of people were killed in that attack alone.

But the defence argued Mungwarere wasn't there that day — and alleged the accusations against him were made up, part of the backlash in Rwanda where those now in government encourage or orchestrate false claims against others in order to exert political control.

The Crown acknowledged that false claims do occur and in fact dismissed some of its own potential witnesses over concerns about their reliability.

But the prosecution argued that enough credible witnesses did come forward to build a case.

The judge said Friday it was not enough for a conviction.