The incident took place just after midnight in Zamboanga, a predominantly Christian province in the Mindanao region. Zamboanga is just a short boat ride from the mainly Muslim Sulu archipelago where Sunday’s church bombing took place. It happened three days after twin bombings at a church on a nearby island killed 21 people.
The military called for unity among Mindanao communities and urged the public to refrain from speculation on social media that could spread misinformation.
Regional task force commander Colonel Leonel Nicolas stressed the incident was "not a retaliatory act."
The attack came a few hours after Philippine President Rodrigo Duterte said on television the twin explosions that killed 21 people on Jolo island may have been a suicide attack.
His comments ran counter to those of other security officials but, if confirmed, it would be one of the first known cases of a suicide attack in the Philippines and consistent with the Islamic State group’s claim made via its Amaq news agency.
The incidents follow a successful and peaceful January 21 referendum that overwhelmingly approved autonomy for the estimated five million inhabitants of predominantly Muslim parts of Mindanao. That followed a decades-long separatist struggle that has killed at least 120,000 people.
Muslims are a minority in the predominantly Catholic Philippines and represent about a quarter of the population of the Mindanao region.
Sectarian violence does not happen often there and the autonomy plan, which aims to address chronic poverty, underdevelopment and violence, is largely supported by Filipinos nationwide.
The Ulama Council of Zamboanga Peninsula condemned what it called a "devilish, irrational and inhumane act" and urged people to be vigilant.
The government believes a faction of the militant Abu Sayyaf group is behind the church bombing. While the group has pledged allegiance to Islamic State, it is comprised of numerous factions with different goals and engages heavily in piracy and kidnapping.