However, the chairman of the Moro Islamic Liberation Front insisted the rebellious faction would not prevent progress in the negotiations with the government, which are scheduled to resume next week.
Ameril Umbra Kato, who is wanted by the Philippine government for leading attacks on Christian communities that killed dozens of civilians in 2008, resigned seven months ago as leader of a guerrilla unit, the movement's chairman, Murad Ebrahim, told reporters at his southern headquarters.
Chief rebel peace negotiator Mohagher Iqbal said Kato resigned as head of a guerrilla command, purportedly for health reasons as he is over 70 years old.
Kato was to have been given a new assignment but instead accused the rebel group of being "revisionist" and formed his own armed group, called the Bangsamoro Islamic Freedom Fighters, Iqbal said.
"It's a problem, and we are trying to address that because that kind of arrangement is not possible," Iqbal told The Associated Press. "There is only one command. We have only one organization, and everybody must toe the line."
He believes the differences with Kato are only over tactics, adding that the upcoming negotiations are compatible with the concept of jihad or armed struggle.
"If we cannot handle this ... we will tell the government that we cannot solve it," he said.
Peace talks brokered by Malaysia are scheduled to resume next week in Kuala Lumpur after they opened last month under the new government of President Benigno Aquino III.
Murad said he was still optimistic "that in a short time we can come out with the proper political formula ... (and) have the beginning of a just peace."
The talks, which seek to end the armed struggle by the 11,000-strong rebel group for Muslim self-rule, have stalled since the August 2008 attacks by Kato's forces following a Supreme Court ruling declaring a preliminary peace accord as unconstitutional.
In a statement he read to reporters at the main rebel camp in southern Maguindanao province's Sultan Kudarat township, Murad reiterated his group's position to seek a "peaceful negotiated political settlement" that would allow Philippine Muslims a degree of self-rule.
Murad warned, however, that "an endless peace process and a 'cease-fire forever' situation are intolerable."
Marvic Leonen, the head of the government peace panel, said they will seek clarifications on the new armed group and the consequences of Kato's "resignation," including whether he will still respect the cease-fire.
He said there can be internal debates within the rebel group and even in the government on "significant issues of policy."
"What matters to us is that a certain kind of discipline is accepted by all those that participate in that kind of a debate, that there is one policy, and that there is one message given by the (rebels), and they maintain to really and truly represent the constituents that they are representing," Leonen told the AP.