The first bomb struck outside a busy shopping mall in General Santos city, on the island of Mindanao. Police say the bomb was hidden inside a tricycle parked near the mall's entrance.
This was followed by a blast in a bus station in the neighboring city of Davao. Later, a bus exploded near a train station in the business district of the capital, Manila, hundreds of miles to the north.
The Philippine military has intensified an offensive in the southern Sulu Archipelago, in a bid to end more than a week of fighting against members of the Abu Sayyaf kidnap-for-ransom group, and other Muslim militants.
Abu Solaiman, the Abu Sayyaf spokesman, quickly claimed responsibility for the blasts, in a telephone call to Manila's GMA Radio.
"Our latest operations in Manila, Davao and Gen San … is our continuing response to the Philippine government's atrocities committed against Muslims everywhere from Manila to Sulu," he said.
Philippine national police chief General Edgardo Aglipay says authorities have been on high alert for terrorist acts since fighting broke out in the south last week. But he says only so much of the country can be guarded.
"We have limited resources," he said. "We have to maximize our coverage where people converge."
The Abu Sayyaf has been engaged in high-profile kidnappings and beheadings of foreign tourists, and has been designated as a terrorist group by the United States.