Shahinon Hapilon, also an Abu Sayyaf commander, was killed in a firefight late Friday at a bus terminal in Guiwan village in downtown Zamboanga City, the police official said, speaking on condition of anonymity.
The body of Hapilon was identified by police informants based on photographs shown to them, the official said.
Hapilon, who carried a P150,000 prize on his head, was the younger brother of Abu Sayyaf commander Isnilon Hapilon, whose group is believed to be holding missionary couple Martin and Gracia Burnham and Filipina nurse Deborah Yap in Basilan.
Western Mindanao police director Chief Superintendent Simeon Dizon said police agents led by Senior Inspector Antonio Monte-bon Jr. had been waiting for Sahilon to surface in Zamboanga City for over a month.
He was cornered while about to board a bus for Ipil town in Zamboanga del Sur.
In Manila, Philippine National Police chief Director General Leandro Mendoza said the killing of Hapilon could eventually lead to the rescue or recovery of the Burnhams and Yap.
The Burnhams were among a group of hostages captured during a raid by the Abu Sayyaf on the upscale Dos Palmas tourist resort off Palawan on May 27 last year.
Most of the hostages have been freed, allegedly in exchange for ransoms, or were murdered.
Some 660 US Special Forces have been deployed since January to advise Filipino soldiers hunting Abu Sayyaf guerrillas in Basilan.
The Abu Sayyaf has been linked by Washington and Manila to the al-Qaeda network of Osama bin Laden, the main suspect in the Sept. 11 attacks on the United States
The government had posted a bounty of P1 million on the head of Shahinon Hapilon. — AFP, Jaime Laude