"A group of our own army men were killed by our own airstrike – 10 killed and 8 wounded," Delfin Lorenzana told reporters, as quoted by the local ABS-CBN radio.
The minister said the government of the Pacific Ocean archipelago was examining the incident.
The attack appears to be part of the ongoing operation to flush Maute militants, affiliated with the Islamic State terror group (Daesh), out of the city on the southern island of Mindanao.
Fighting broke out in Marawi last month when Islamists stormed the city, prompting Philippine President Rodrigo Duterte to declare martial law on the island. More than a hundred, including militants, have died in clashes.