Spokesman Maj. Filemon Tan Jr. said Tuesday that the fatalities included around 60 Abu Sayyaf members killed in the island province of Sulu and another 52 in nearby Basilan.
He added 19 militants were wounded and 30 others captured in Sulu, while 10 were reportedly wounded and 68 others were either captured or surrendered in Basilan.
On the military side, 22 soldiers were killed in Sulu and six in Basilan, with a total of 36 other troops wounded in action.
The military’s regional spokesman revealed the number of casualties on both sides a day after President Rodrigo Duterte -- who has ordered security forces to “destroy” the Abu Sayyaf -- traveled to Sulu to visit soldiers wounded during weekend clashes.
Duterte awarded each of the six wounded soldiers at a hospital in Camp Teodulfo Bautista in Jolo town a Wounded Personnel Medal.
Since 1991, the Abu Sayyaf -- armed with mostly improvised explosive devices, mortars and automatic rifles -- has carried out bombings, kidnappings, assassinations and extortions in a self-determined fight for an independent province in the Philippines.
It is notorious for beheading victims after ransoms have failed to be paid for their release.
The Abu Sayyaf is among two militant groups in the south who have pledged allegiance to Daesh, prompting fears during the stalling of a peace process between the government and the country's one-time largest Moro rebel group that it could make inroads in a region torn by decades of armed conflict.