The explosion happened as soldiers and pro-government militia troops were inspecting a van that was stopped at the checkpoint just after dawn, said military spokesman Lieutenant Colonel Gerry Besana.
The powerful blast killed at least one soldier and several militia troops on the outskirts of the mainly Christian city of Lamitan, which is on the predominantly Muslim island of Basilan, he added.
Authorities have launched an investigation of the blast, with speculation over the circumstances of the blast.
"The suspect detonated the bomb sensing danger he will be captured," local official Mujiv Hataman told AFP.
Basilan is a stronghold of the Abu Sayyaf group, an Al-Qaeda-linked group blamed for the archipelago’s deadliest bombings.
It is among several armed groups fighting government forces in the southern Philippines in decades-long rebellion that has claimed more than 100,000 lives by government count.
President Rodrigo Duterte recently signed a law to create greater Muslim autonomy in the south which is hoped to end the conflict. — AFP/VNS