Regional military spokesman Maj. Filemon Tan said 22 militants had been killed and 16 others wounded in the assaults that started last week in the jungles of Sulu, a predominantly Muslim province where the ransom-seeking militants are also believed to be holding a number of foreign hostages.
One soldier had been killed in the fighting in impoverished Sulu, about 590 miles (950 kilometers) south of Manila, he said.
The thousands of troops waging the assaults were backed by rocket-firing helicopters and artillery fire.
President Rodrigo Duterte, who started his six-year term on June 30, has warned the Abu Sayyaf to stop a wave of ransom kidnappings, saying he would eventually confront them. His military chief said last week a looming offensive would "shock and awe" the extremists.
While past presidents have regarded Abu Sayyaf militants as bandits thriving on kidnappings for ransom and extortion, Duterte said last week he would not lump them with criminals.
The militants, however, have shown no sign of heeding Duterte's call to stop kidnappings, which he said has sullied the country's image.
Indonesian officials said today that suspected Abu Sayyaf gunmen kidnapped three Indonesian fishermen over the weekend off Lahad Datu in the Malaysian part of northern Borneo, the latest among several offshore attacks that have sparked a regional security alarm.
Washington and Manila list the Abu Sayyaf, which has more than 400 armed fighters, as a terrorist organization for deadly bombings, ransom kidnappings and beheadings over the last three decades.
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