There were no immediate reports of any fatalities in the second explosion, but at least two people were reported to be injured.
In the latest explosion, an improvised bomb was left by a road in Cotabato City on Mindanao island and was picked up by rubbish collectors.
Peraco Macacua, the city police chief, said that one person died on the spot when it exploded, and six others were taken to hospital.
The first explosion happened at about 6pm (10:00 GMT) in the trade hub in the south, where Muslim and communist armed groups are fighting long-running rebellions.
Police said it was premature to blame the attack on any group.
German Doria, the regional police chief, said that the crude bomb was left on the side of a road near a crowded lottery outlet in the market.
Hospital staff said among the dead were two children, boys aged eight and 12.
Police conducts rescue exercise in Cebu during
security training for the Asean summit [AFP]
Pascual Peroy, a police officer, said the second blast was caused by an improvised bomb placed near the perimeter fence of a police outpost along the city's national highway.
It went off at about 8:40pm (12:40 GMT), just after police on duty left the outpost to go on patrol, he said.
A man seen walking near the police outpost was wounded and another male passer-by was hit by shrapnel, Peroy said.
Western governments had given warning that armed groups might bomb a summit of the Association of South East Asian Nations and a wider meeting of East Asian leaders from January 13 to 15 in the central Philippines or attack cities in the south.
Manila, which holds the rotating chairmanship of Asean, had postponed the original Asean summit last month, ostensibly due to a typhoon but days after the Australian, US and British embassies said that terrorists would try to disrupt it.
Philippine police said there was no specific threat in the central island of Cebu, guarded by about 13,000 police and soldiers, but put the entire country on high alert.
Doria said the bombing may have been retaliation by local Muslim group Abu Sayyaf for recent military killings of some of its senior members.
He also said Abu Sayyaf may have planted the bomb to divert the military from flushing them out of the remote southwestern island of Jolo.
At least 7,000 soldiers and some US military advisers are on Jolo, a sprawling, mountainous island, to combat Abu Sayyaf.
The meeting on the resort island of Cebu will be attended by leaders from Japan, China, India, South Korea, Australia, New Zealand and the 10-member Association of South East Asian Nations.
Asean comprises Brunei, Cambodia, Indonesia, Laos, Malaysia, Myanmar, the Philippines, Singapore, Thailand and Vietnam.