The UN's Ivory Coast mission says three mass graves containing at least 99 bodies have been found near the northern rebel-held town of Korhogo.
The UN is deploying 6,000 peacekeepers to Ivory Coast
The town was the scene of fighting between rival factions in June.
A UN statement said some of the dead had been shot, but it quoted witnesses as saying others had been suffocated.
The discovery came two days after rebels, who seized control of the north of the country in 2002, signed a deal to rejoin the government.
Asphyxiation and bullet wounds
The New Forces, as the rebels are now known, stopped fighting the government 18 months ago, but there were clashes between rival rebel factions on 20 and 21 June in Korhogo.
Forces loyal to the New Forces leader Guillaume Soro gained control of the town in gun battles that left 22 people dead.
They blamed the violence on an assassination attempt on Mr Soro by his Paris-based rival Ibrahim Coulibaly, known as IB.
Subsequent allegations of mass human rights abuses led to the UN investigation, which found up to 99 bodies in three different sites.
"Obviously the United Nations cannot remain silent in face of these kinds of abuse. Some were asphyxiated, some died of bullet wounds," Jean-Victor Nkolo of UN's mission in Ivory Coast told the BBC's Network Africa programme.
The UN has stressed that the New Forces have co-operated with the investigation.
But the UN says it is concerned about the fate and unconfirmed number of prisoners still held by the New Forces.
According to the BBC's James Copnall in Abidjan the New Forces have refused to comment on any of the allegations until they have officially received a copy of the report.
Human rights groups say serious abuses have been continuing in both government and rebel-held areas.
An international commission of enquiry arrived in Ivory Coast last month to start a full investigation into all human rights abuses since the start of the crisis.
All sides of the political divide committed themselves to helping the enquiry at last week's summit in Ghana to relaunch the flagging Ivorian peace process, our correspondent says.