The military said Edoh Abdulah, 45, was hit four times and died on the spot.
He was shot outside the residence of senior MILF vice chairman for political affairs Ghadzali Jaafar in Barangay Crossing Simuay, in Isulan.
Authorities initially believed that personal grudge could be a motive for the killing.
A massive manhunt has been launched for the arrest of the killer.
MILF spokesman Eid Kabalu told reporters Abdulah was a member of the MILF peace panel and a commander of the rebel group’s 104th Command based in Sultan Kudarat. "He was there to strengthen the local peace agreement with the government," he said.
Abdulah was a resident of Laguilayan Village also in Isulan, and may have been tailed from his residence to Jaafar’s house by the assailant, Kabalu said.
Reports reaching Camp Aguinaldo said police were still investigating if the gunslaying was "political" in nature or if there was a personal motive behind it.
In an interview with defense reporters, Kabalu did not rule out the possibility that the police and the military might have had a hand in the killing in an attempt to weaken the peace negotiations between the government and the MILF.
But Kabalu was quick to point out that the incident would not directly affect the ongoing ceasefire agreement between the MILF and the government, as well as peace talks to be held in Kuala Lumpur, Malaysia within the month.
"The killing has nothing to do with the ceasefire agreement," he said.
Ghadzali also believed that the murder was not connected to the victim’s role in the peace talks. "We are convinced that the motive for his murder was personal."
"We are shocked, but all we can do is request the police to investigate deeper into the case," Jaafar added.
He also pointed out that Abdulah was busy coordinating with members of the MILF ceasefire committee in connection with today’s start of the joint government-MILF inquiry into the Dec. 24 bombing in Datu Piang town in Maguindanao that killed the town’s mayor, Datu Saudi Ampatuan, and 17 other people.
The military has tagged an MILF band led by Commander Rambo as the perpetrators of the bomb attack.
Meanwhile, observers noted that the killing of Abdulah happened after the Armed Forces of the Philippines pointed to the MILF as behind the series of explosions and attacks in Central Mindanao that killed several people and wounded scores of others last year.
The 12,000-strong MILF is the country’s largest remaining Muslim guerrilla force fighting for the establishment of an independent Islamic state in the south since 1978.
It signed a ceasefire with Manila in 2001 to pave the way for peace talks, but sporadic clashes between the military and MILF guerrillas in remote areas have persisted.
It was not clear how the killing could affect the peace negotiations.
Meanwhile, another MILF rebel identified as Ebs Omar was killed in an encounter yesterday between the MILF and the military in Datu Piang.
The clash took place at 10:30 a.m. when elements of the Army’s 37th Infantry Battalion in Barangay Kitango crossed paths with a 10-member MILF team led by one Commander Amilil Umbra Kato.
The troops seized a 12-gauge shotgun during clearing operations while nobody from the government side was injured. — With AFP report