There was no immediate word on the cause of two of the three blasts but a police officer said Muslim separatists being pursued by soldiers on a southern island might be trying to create a diversion.
"There was a loud explosion. The ground was shaking. The people were screaming and running in all directions," said a witness in General Santos City.
Witnesses said the blast in General Santos City on Monday destroyed a parked motorcycle outside a shopping mall, killing three people.
About 15 wounded people were taken to hospital.
In Davao City, also in the troubled southern Philippines, a grenade exploded at a bus terminal at almost the same time, wounding five people, police said.
About half an hour later, a blast went off in the Makati central business district of the capital, Manila. One witness, said smoke had been seen coming from below an elevated-train station.
"We were expecting something but we could not predict when and where it would take place"
Military intelligence official
Chief Superintendent Antonio Billiones, a regional police chief, said the attacks could be a diversionary ploy by Muslim separatists battling government forces on Jolo island.
"We're still investigating," he told reporters. "But, we can link the attack to what is happening in the mountains of Jolo."
Nearly 5000 soldiers were fighting about 800 separatists from the al Qaida-linked Abu Sayyaf group and rogue members of the Moro National Liberation Front on Jolo.
"Based on our assessment, the attacks were in revenge for the air strikes on a suspected militant hideout in Liguasan marsh last month," a military intelligence official said.
"We were expecting something but we could not predict when and where it would take place."
On 12 December, a bomb exploded at a market in General Santos City killing 14 people and wounding 65. Officials linked that attack to an air strike on a separatist hideout.