The UN and Western governments brokered the deal on January 23 in the hope of establishing a lasting peace in an area of the country where violence has continued beyond the formal end of the DRC's 1998-2003 civil war.
The pact, barely a month old, has already been strained by renewed skirmishes.
Nkunda's move came in response to UN allegations his Tutsi fighters had killed at least 30 Hutu civilians while the peace deal was being negotiated.
He said his representatives would suspend their participation in the commission, set up to hammer out the technical aspects of the peace deal, until an independent inquiry had been launched.
"We are demanding these things be verified by a mixed investigation made up of the government, the UN, and us," Nkunda was reported by the Reuters news agency as saying.
A report by UN rights investigators, which became public this week, alleged that Tutsi fighters loyal to Nkunda had killed at least 30 Hutu civilians.
The report alleged the Hutus were shot, hacked with machetes, or beaten to death with hammers on January 16 and 17 around Kalonge, about 100km west of Goma, the capital of east North Kivu province.
Nearly all the victims were men, though a one-year-old baby, a 14-year-old boy, and a woman were also killed, according to the report.
Nkunda denied his group was involved in the alleged massacre, saying the UN was "spreading rumours, and we cannot accept that this continues".
But a spokesman for Nkunda's National Congress for the Defence of the People (CNDP) said the move did not mean the group was withdrawing definitively from the ceasefire and peace pact signed last month.
While announcing its withdrawal from "all meetings relating to the Act of Engagement", as the January 23 deal is known, the CNDP said it would to co-operate with international mediators to clear up the massacre allegations.
There was no immediate reaction to Nkunda's statement from the UN Mission in Congo (MONUC), which has 17,000 peacekeeping troops in the vast, mineral-rich former Belgian colony.
Despite the signing of January's peace deal and the creation of around 30 UN peacekeeping bases in a buffer zone between the warring factions, almost daily clashes have been reported between forces loyal to Nkunda and Mai Mai fighters.