Police in the country say two people are in a critical condition after the attack in North Cotabato province late on Wednesday.
Four other parishioners at the United Church of Christ were injured in the incident.
Detectives say they are not sure if Muslim rebels are to blame.
Police in the country have been on alert for attacks from extremists since a peace deal was signed between the government and an Islamic insurgent group.
The agreement, which would establish a more powerful autonomous region for Muslims in the south, has been rejected by some extremists.
The Philippines is a mainly Catholic country.