The fighting occurred as negotiators for the Philippine government and the Moro Islamic Liberation Front (MILF) met in Kuala Lumpur to discuss details of a preliminary peace deal signed in October.
Four soldiers were wounded when the guerrillas strafed a vehicle transporting the troops in Guindulungan town in Maguindanao province, 960 kilometres south of Manila, said Colonel Dickson Hermoso.
The rebels belonged to a faction of the MILF that is against the peace talks with the government, Hermoso said.
The government and the MILF signed the framework peace agreement in October, which calls for the creation of a new Muslim autonomous region on the southern island of Mindanao in 2016.
Negotiators extended their meeting in Kuala Lumpur for a sixth day on Saturday to try to finalise details of the deal.
Officials said the teams were deadlocked on how the national government and the autonomous region would share financial resources.