Air strikes and artillery pounded an area in the Liguasan marsh in Maguindanao, where the Bangsamoro Islamic Freedom Fighters (BIFF) group had been making improvised explosive devices, said Brigadier General Cirilito Sobejana.
About 60 to 100 BIFF militants were in the vicinity when the assaults began before dawn, Sobejana said.
"Fifteen were confirmed killed, 10 were injured and two others were captured," he said. "We were able to destroy their main IED factory in southern Liguasan, and this is a big loss to them."
The military classifies the BIFF, which it say has 300 to 400 members, as a terrorist organisation, along with the Abu Sayyaf and Maute groups.
The militants in southern Philippines have regrouped and were retraining and recruiting new members for future attacks after occupying the southern city of Marawi for five months last year, the military has said.