Rwanda's President Paul Kagame, long a favourite of successive American administrations, may find himself targeted by President Barack Obama's special war crimes envoy over increasingly stark evidence of Rwandan involvement in the rape, pillage and brutal ethnic killings by militias operating just across the Rwandan border inside Congo.

Mr. Kagame, the Tutsi leader who returned to genocide-ravaged Rwanda after the 1994 massacres and set about building a booming, modern, African state that won him praise and accolades has slowly alienated western powers with his increasingly dictatorial ways.

The Rwandan president has repeatedly dismissed all suggestions that his army is involved, directly or indirectly, in backing or directing the brutal militias in eastern Congo. He calls the accusations "fictitious" and pointedly says "Rwanda has its own problems."

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But evidence is mounting linking Mr. Kagame regime to the militias.

The Obama administration had already cut off funding for some aid programs – including media building – after the lopsided 2010 election in which Mr. Kagame won more than 90-per cent of the vote, while several opposition figures died mysterious and violent deaths. Earlier this month, Washington scrapped a modest military aid program in its latest signal of displeasure with the government in Kigali.

That produced the usual, angry and absolute denials of any Rwandan wrongdoing from Mr. Kagame's blunt-speaking Foreign Minister Louise Mushikiwabo. The Obama administration's decision to cut off military aid "is based on bad information, and is wrong on the facts," she said. "Rwanda is neither the cause nor the enabler of instability in the eastern DRC."

Now comes the carefully worded but unmistakable warning about war crimes culpability that seems certain to enrage the prickly Rwandan president who curries U.S. favour and even arranged for his son to attend the elite U.S. military academy at West Point. It came earlier this week from Stephen Rapp, the Obama administration's special representative for war crimes.

In an interview with The Guardian, Mr. Rapp fired what amounted to warning shots at Mr. Kagame, his Defence Minister James Kabarebe and the generals playing key roles in his shadowy security apparatus.

Pointedly referring to the recent conviction of former Liberian President Charles Taylor, now serving 50 years for aiding and abetting war crimes committed in neighbouring Sierra Leone, Mr. Rapp said: "There is a line that one can cross under international law where you can be held responsible for aiding a group in a way that makes possible their commission of atrocities."

He stopped short of saying Mr. Kagame had crossed the line, although a recent UN report determined Rwanda was involved in funding, arming, organizing and helping recruit for the murderous militias, including the notorious M23 rebels that have slaughtered thousands and driven hundreds of thousands from their homes in eastern Congo.

"I'm not sure if we are there in terms of criminal conduct," Mr. Rapp told the Guardian. "But if this kind of thing continued and groups that were being armed were committing crimes … then I think you would have a situation where individuals who were aiding them from across the border could be held criminally responsible."

The UN report concluded Rwanda was supporting seven armed rebel groups in Congo. M23 is the most powerful and now controls a swath of strategically important territory near the city of Goma in eastern Congo, just across the border from Rwanda.

The UN group said it had established "a systematic pattern of military and political support provided to the M23 rebellion by Rwandan authorities."