The military launched the operation against the Bangsamoro Islamic Freedom Fighters (BIFF) last month in a marshy, farming region on Mindanao island, where Muslim rebels have for decades fought for independence.
"One of the cadavers is a foreign-looking guy," said military spokesman Brigadier-General Joselito Kakilala, outlining the operation in an interview aired on ABS-CBN television.
The corpse's features bear "similarities" to one of the United States' "most wanted" Islamic militants, he said, refusing to identify the suspect.
The raid followed a bloody anti-terror operation in January that the Philippines says killed Malaysian militant Zulkifli bin Hir, one of Asia's most wanted men, but also claimed the lives of 44 police commandos.
The BIFF and other rebels killed the commandos as the operation backfired, triggering a wave of outrage in the Philippines that has shaken the administration of President Benigno Aquino.
The fighting centres on the Liguasan marshlands of the south, where Filipino militant Abdel Basit Usman, one of the terror suspects sought by the US, survived the January 25 police raid.
In addition to the suspected militants killed in the operation, which is expected to end this week, four were arrested and some 33 wounded, Kakilala said.
"We also got their bomb factories," he added.
The fighting has forced about 45,000 civilians to flee their homes, according to local officials.
The BIFF is now believed to number less than 300, but their leader, Ameril Umrakato, "remains very influential" in the area, he added.
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