The air raid took place on Thursday in an area known as a militant stronghold.
Reports said one Abu Sayyaf leader and two from the Jemaah Islamiyah (JI) group were killed, including Malaysian Zulkifli bin Hir, or Marwan.
He was on the US FBI’s most wanted list, with a $5m (£3.2m) reward offered for his capture.
Regional military commander Maj Gen Noel Coballes told Agence France Presse news agency that troops on the ground had confirmed the deaths of “Zulkifli bin Abdul Hir, alias Marwan; Mohammad Ali, alias Muawiyah; and Abu Sayyaf leader Abu Pula”.
According to the military, the militants were killed in the town of Parang in Jolo, the capital of Sulu province in the Mindanao region.
Marwan is said to have been behind a series of bomb attacks in the southern Philippines since 2006.
According to the FBI, he is “an engineer trained in the US” and has conducted bomb-making activities for militant groups, especially the Abu Sayyaf.
Abu Sayyaf is the smallest and most radical of the Islamic separatist groups in the southern Philippines.
JI has links to al-Qaeda and has a long track record of bomb attacks in Indonesia. It is believed to have been behind the Bali bomb attacks of 2002.