One of two men on the motorcycle threw the grenade into the Roman Catholic church in a suburb of the city of Zamboanga just as a group of senior citizens were meeting there, police and district officials said.
Four senior citizens and one passer-by were injured, said district chief Jodifer Arquiza.
"It (the motive) is unlikely to be personal. What can they get from these senior citizens? Perhaps this is a message," he told reporters.
The local police chief, Chief Inspector Felixberto Martinez, said they were pursuing all possible leads but could not give a motive for the attack.
The bombing came days after troops elsewhere in Mindanao island launched a major operation against a breakaway Muslim rebel group opposed to peace talks with the main Muslim rebel organisation, the Moro Islamic Liberation Front (MILF).
Zamboanga City was also the scene of a bloody siege in September by another Muslim armed group which feared that the peace talks with the MILF would sideline them.
More than 240 people were killed in the three weeks of fighting in Zamboanga, a city with a mixed Christian and Muslim population.
Despite the threats of violence, government and MILF negotiators on January 25 announced that they had successfully completed talks aimed at ending a decades-long Muslim insurgency that claimed tens of thousands of lives.
President Benigno Aquino recently said the government would crush "spoiler" rebels that might try to derail the peace process with the MILF.