KIGALI, Nov 13 (Reuters) - Rwandan President Paul Kagame on Monday denied his troops would invade neighbouring Congo to flush out thousands of Hutu rebels hiding there.

Media reports quoted Kagame, who has had bitter relations with Democratic Republic of Congo in the past, as saying while in Japan last week that he was ready to send troops back into Congo it if failed to rein in militias there.

Kagame's army invaded Congo twice in the late 1990s saying it wanted to hunt down ethnic Hutu militiamen who led Rwanda's 1994 genocide, which killed 800,000 Tutsis and moderate Hutus.

"What they reported was ... not what I said," Kagame told reporters in Kigali after a week-long visit to Asia. "In the press conference I addressed and in the speeches I delivered, there was no single mention of us going back to Congo."

"What I said was that if we were attacked by anybody from Congo, we would do what any country would do to protect itself," he added, without any further explanation.

Critics have accused Kigali of sending troops to plunder mineral-rich Congo's natural resources.

"If we were to go back to Congo, I would be frank about it," added Kagame, a Tutsi whose rebel group defeated Hutu militias to end the 1994 killings.

Congo, struggling to emerge from years of war, is awaiting the official result of an Oct. 29 presidential run-off, due this week.

Returns filed by polling stations have indicated incumbent President Joseph Kabila leading with around 60 percent of the vote, while his rival, Vice-President Jean-Pierre Bemba, had 40 percent.

"Whoever wins, we will work with him to resolve the problems of Interahamwe," Kagame said referring to the Hutu militia.

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