Mohagher Iqbal, chief negotiator for the MILF, said the only option left for the separatists was to take the accord to the United Nations and the Organisation of the Islamic Conference to seek their guarantees that if talks resume their outcome will be respected.
"We will bring it to a forum where the voices of the Moros will be heard," he said.
He criticised the government of Gloria Arroyo, the president, for backing out of the deal after 11 years of negotiations, and warned that militants among the separatists opposed to the peace process may stage fresh attacks.
"After long years, we came to a point that seemed to bolster what the anti-negotiation groups are saying: that the government could not be trusted," Mohagher Iqbal said.
The MILF has been battling for self-rule in the predominantly Roman Catholic nation's volatile south for decades.
Despite the latest setback, both sides said they will respect a 2003 ceasefire, which has been monitored by a handful of international observers.