An internal UN report seen by the BBC 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.
The conflict broke out in April after a mutiny by some Congolese army officers.
Rwanda’s foreign minister told the BBC the UN report is “categorical lies”.
“The UN mission in DR Congo is lying; they have not verified anything; they are repeating claims and rumours that we, the Rwandan government, have heard over the last many weeks,” Foreign Minister Louise Mushikiwabo told the BBC’s Network Africa programme.
“What would Rwanda gain in creating instability around its own borders? It does not make sense,” Ms Mushikiwabo said.
The UN report says some of the leaders are Tutsi officers who had been linked to Rwanda.
They were incorporated into the Congolese army in 2009 as part of a peace agreement.
The area has suffered years of fighting since the mid-1990s, when over a million ethic Hutus fled across the border into DR Congo following the Rwandan genocide.
Tens of thousands have fled the recent violence in the east of the country.
The BBC’s Gabriel Gatehouse, in the eastern Congolese city of Goma, says the UN spoke to 11 defectors there.
They had deserted their posts in the mountainous jungle area on the border between the DR Congo and Rwanda.
The UN report says the deserters were Rwandan nationals, recruited in Rwanda under the pretext of joining the Rwandan military.
They were given weapons and training, and were then sent into DR Congo.
Some of the men were recruited as early as February 2012, the report says.
This is a potentially significant detail, our correspondent says: if the claim is true, it would suggest Rwanda was preparing for conflict before the mutiny by rebellious officers began in April.
One of the deserters, the report says, is a minor.
Earlier, there was fresh fighting between government forces and the army mutineers.
A spokesman for the mutineers, Vianney Kazarama, told AFP that the Congolese army was attacking one of their strongholds in Nord-Kivu province with heavy weapons.
The mutineers say they belong to the March 23rd Movement which originated from an armed ethnic Tutsi group, the CNDP.
They agreed to be integrated into the Congolese army under the 2009 peace accord but recently started to defect en masse, complaining of bad treatment.
Bosco Ntaganda, who is known as the “Terminator” and wanted by the ICC for alleged war crimes, is accused of masterminding the mutiny. He denies the claim.
Before the peace deal, the CNDP militia threatened to invade Goma, leading some 250,000 people to flee.
People in and around the town of Goma blame these troops for persistent unrest – including looting and rape – since the formal end of DR Congo’s war in 2003.