The accident happened when a plane bombing rebel positions in the city of Marawi missed its target and knocked down buildings on to the soldiers, a military spokesman, Lieutenant Colonel Jo-Ar Herrera, said in a statement.
"Large debris from heavily reinforced buildings accidentally hit two of our personnel," Herrera said. "We are saddened by this unfortunate incident."
He said 11 soldiers sustained minor shrapnel wounds and were recuperating in the hospital.
An air strike on Islamist rebels killed 11 government troops in May.
Militants linked to Islamic State seized Marawi on May 23 and have been resisting daily assaults by government forces using aircraft and artillery.
President Rodrigo Duterte said on Tuesday he needed 15 more days to defeat the militants.
More than 500 people have been killed, including 389 militants, 90 members of the security forces, and 39 civilians, since the fighting erupted. About 260,000 residents have been displaced.
Militant members of the Maute group, an ISIS-affiliated group, inside a house in Marawi. File picture
A Philippine government air strike aimed at Islamist rebels mistakenly killed two soldiers on Wednesday, the military said, the second such deadly accident in a bloody campaign to oust the militants from a southern city.
