A possible split in the ranks of the Moro Islamic Liberation Front could threaten the effectiveness of the peace talks, which resume Wednesday in Malaysia.
Government negotiator Marvic Leonen spoke cautiously about the status of Ameril Umbra Kato, a rebel commander who the movement's leaders said over the weekend had formed his own armed group - called the Bangsamoro Islamic Freedom Fighters.
"The government panel views the reported resignation of a known commander of the (rebels) with serious concern," Leonen said in a statement, adding the government would ask about the status of Kato in the Malaysia talks.
The peace process, which seeks to end the decades-long rebellion by the 11,000-strong rebels who seek autonomy for a southern, mostly Muslim region, has stalled since the August 2008 attacks led by Kato and two other rebel commanders following a Supreme Court ruling declaring a preliminary peace accord as unconstitutional.
Kato resigned from the 105th base command seven months ago, the rebels say.
He was to have been given a new assignment but instead accused the rebel group of being "revisionist" and formed his own armed group, chief rebel peace negotiator Mohagher Iqbal said on Saturday
The rebel leadership is trying win back Kato through dialogue, rebel spokesman Eid Kabalu said.
Kato has had differences with rebel leaders in the past. In 2005, his command was briefly deactivated after it launched an unauthorized assault on soldiers, who were pursuing suspected militants belonging to the Southeast Asian militant network Jemaah Islamiyah, Kabalu said.
He is wanted by the government for leading deadly attacks on Christian communities in 2008 and has been accused by security officials of having links with Indonesian and other foreign extremists in the volatile south.
Authorities looking into a Jan. 25 bus bombing that killed five people in the capital's Makati financial district have considered the possibility that Kato may have played a role in the attack due to his rejection of the Malaysian-brokered talks and links to past bombings, two security officials have said on condition of anonymity because they were not authorized to deal with the media.
The rebel front has denied any role in the bus bombing.
Government negotiator Leonen said the administration of President Benigno Aquino III still hopes to forge a peace deal with the Moro Islamic Liberation Front "within the soonest possible time" but wanted to be sure that both sides "can deliver a just and lasting peace."
Washington and other countries have supported the talks, saying these could turn battlefields into economic growth areas rather than breeding grounds of militants that could wage attacks beyond the Philippines.