The Sikorsky S-76A took off from southern Zamboanga city for a flight to nearby Sulu province and crashed in rainy weather in the hilly village of Upper Manggas on Basilan island, the air force and police said.
The two pilots and two other crew members were killed.
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They were bound for Jolo town to airlift troops who were wounded in two August 24 bombings blamed on Abu Sayyaf militants.
The bombings killed 15 people, including soldiers, along with two suspected female militants, and wounded more than 70 soldiers, policemen and civilians.
Officials were investigating the cause of the crash and other Sikorsky helicopters were grounded for safety checks while the investigation is under way.