The powerful explosion, claimed by the Daesh group, occurred after soldiers and pro-government militiamen stopped the vehicle just after dawn to search it.
One soldier, five militiamen and four civilians were killed on the outskirts of the mainly Christian city of Lamitan, which is on the predominantly Muslim island of Basilan.
The van driver, a suspected member of the Abu Sayyaf militant group, also died, Philippine military spokesman Colonel Edgard Arevalo told reporters in Manila.
He said government forces had been on heightened alert after receiving reports that extremists planned to plant improvised explosives around the island.
"We can just imagine the tragedy that this would bring to the people of Basilan had we not stopped them at the checkpoint," he said.
Authorities earlier said at least five people died in the blast.
Basilan is a stronghold of the notorious Abu Sayyaf kidnap-for-ransom group.
'War crime'
It is one of several armed groups fighting troops and police in the southern Philippines, where a decades-long rebellion has claimed more than 100,000 lives by government count.
Roderick Furigay, the Lamitan vice mayor, speculated that the explosives could have been intended for a parade on Tuesday morning by 4,000 children in the centre of the town to mark the country´s "nutrition month".
"That could have been (the target)," he said on ABS-CBN television. "It´s a good thing they were stopped at the checkpoint."
President Rodrigo Duterte recently signed a law to create an autonomous region in the south to help end the conflict.
Duterte put the southern Philippines including Basilan under martial rule until the end of this year after Abu Sayyaf members based on the island joined pro-Daesh militants who seized the southern city of Marawi last year.
The five-month siege killed 1,200 people and destroyed much of the centre of the city.
Daesh´s propaganda arm Amaq, claiming responsibility for Tuesday´s blast, said "a suicide attack has killed around 15 from the Philippine army" in Lamitan.
Duterte spokesman Harry Roque condemned the Basilan blast, describing it a "war crime" apparently aimed at civilians.
"We condemn in the strongest possible terms the latest terrorist attack in Basilan perpetrated in violation of our laws," Roque said in a statement.
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