Abdul Lim was fatally shot after handing over $12,000 to the kidnappers near the town of Patikul in Jolo, Sulu, police said.
Lim’s body was found last week, but it was not exactly clear when he was killed.
The money Lim delivered was meant to pay for the freedom of Gertrudes Tan, a relative reportedly kidnapped by the Abu Sayyaf in April who is believed to still being held in the jungles of Jolo.
"The operation is ongoing and we are trying to locate Gertrudes Tan. There are many intelligence reports and some of them said Tan is sick and suffering from respiratory disease," police Chief Superintendent Acmad Omar said.
The Abu Sayyaf is a small group of Muslim kidnappers branded by both Manila and the US government as a terrorist organization. It has been blamed for a series of deadly raids and bombings in the south as well as the murders of two American hostages in the last two years.