An unpublished report by UN experts has alleged that the Rwandan military has been supporting the mutineers.
But Louise Mushikiwabo said such allegations were endangering the safety of Rwandans in eastern DR Congo.
She made the comments during a visit to the UN and said Rwanda was urging rebels to negotiate rather than defect.
Tens of thousands have fled the recent violence in eastern DR Congo.
The internal UN report seen by the BBC also cited defecting soldiers who said they had been trained in Rwanda under the pretext of joining the army, before being sent over the border to fight.
"Of course Rwanda's top army leadership in no way, and I'm very categorical about this, in no way would be involved in destroying the peace they have been working very hard to build," Ms Mushikiwabo told journalists in New York.
She said the allegations were already creating a dangerous climate for Rwandan citizens in DR Congo,where 11 men had been captured and beaten last week.
The foreign minister also expressed concern about inflammatory anti- Rwanda rhetoric in Congolese and other African media.
The Congolese government has written to the UN Security Council, demanding that the UN's evidence be published, and that it pressure Rwanda to halt any support for the mutineers.
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