Military spokesmen said a bomb hit the soldiers' convoy as it drove on a road in a southern region where an armed group which had pledged allegiance to the Islamic State (IS) group operated, wounding nine.
"My advance party was ambushed a while ago. The Presidential Security Group was hit by an IED (improvised explosive device)," Duterte said in a speech during a visit to a northern Philippines military camp.
The convoy that was attacked in Marawi city also included local troops as well as staff members of the presidential communications office, though no civilians were hurt, military officials said.
The planned Duterte visit came days after the military began operations against dozens of armed members of the Maute group holed up in an abandoned government building in the mainly Muslim rural town of Butig on Mindanao island.
Fifteen soldiers were injured in the fighting while 35 militants were killed, military spokesman Brigadier-General Restituto Padilla told AFP.
The ambush came a day after the police said the Maute group left a bomb near the US embassy in Manila which authorities later safely exploded.
The Maute gang was also blamed for a bombing in Duterte's home town in the southern city of Davao in September that killed 15 people.
Padilla said it was likely the Maute group was behind the ambush.
"We know their supporters are surrounding the area and possibly planted bombs on the side of the roads to disrupt the movement of troop reinforcements," Padilla said.
Yesterday, Duterte said IS, which controlled vast swathes of Iraq and Syria, had linked up with the Maute gang, a departure from previous military denials of formal links between IS and local extremist groups.
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