Police also blew up five suspicious packages and were checking whether they contained bombs that failed to detonate.
There was no claim of responsibility for the attacks, but a military spokesman said the initial suspect in the bombings was the Muslim guerrilla group Abu Sayyaf. The group has previously threatened attacks in retaliation for an ongoing military offensive against it.
Lt. Col. Danilo Servando also said there were similarities between Thursday's bombings and an Oct. 2 explosion in Zamboanga which killed four people, including an American Green Beret. Officials blamed the earlier blast on Abu Sayyaf.
TNT apparently was used in both attacks.
Servando said suspicion fell on an Abu Sayyaf faction headed by Khaddafy Janjalani, one of five group leaders indicted by Washington for a mass kidnapping last year that left 18 hostages dead, including a Kansas couple.
"There is no solid basis to pin the blame on Janjalani's group but it's one of the groups that has been sowing terror in the south," Servando said.
Ten people, including two foreigners, were brought in for questioning after Thursday's explosions, police said.
President Gloria Macapagal Arroyo immediately condemned the latest terrorist strike to hit her impoverished country.
National Security Adviser Roilo Golez said officials considered the Zamboanga attack "a local concern" that did not require a state of emergency.
"The public has nothing to worry about," Golez said.
The first blast occurred at 11:30 a.m. at the five-story Shop-o-Rama department store, and was followed a half-hour later by a second blast at an adjacent store. Police Chief Mario Yanga said the bombs were left at counters where shoppers leave packages as they enter.
Mayor Maria Clara Lobregat said the Zamboanga City Medical Center received three dead victims and 50 wounded, many of them seriously.
The usual noontime bustle of Zamboanga's downtown area became a gory scene of scattered debris, blood and chaos.
"The ground shook and pandemonium broke out. People bathed in blood were all screaming and running away from the smoke," said Ofelia Fernandez, who was across the street from the Shop-o-Rama.
Television footage showed victims being hauled out of the bombed buildings' lobbies on stretchers. A bloodied man, with most of his shirt and pants ripped away by a blast, staggered out with the help of a policeman.
Firefighters poured water onto wreckage as medical workers rushed people on gurneys to waiting ambulances. Police cars and pickup trucks also were used to ferry victims from the area. None of the victims were believed to be foreigners.
A truckload of soldiers arrived to secure the area, and military canine units were brought in to sniff for other possible explosives. Two MG-520 attack helicopters hovered overhead as armored personnel carriers patrolled the ground. Checkpoints quickly were established.
All shops in the city's commercial center closed, and police advised people to stay out of the area, blocking off streets with cars and yellow tape. Trapped employees were later let out, one by one, helped by police. Many schools around the city sent students home.
Most public buildings in metropolitan areas in the Philippines have armed guards at entrances, sometimes with metal detectors, who are supposed to search packages. But Yanga said they often become complacent in their searches.
"These malls are always being lectured, but their security remains lax," he said.
Zamboanga, a mostly Roman Catholic city of about 600,000, is in the heart of the predominantly Muslim southern Philippines.
Philippine officials have linked the Abu Sayyaf to al-Qaida, citing alleged attempts by Osama bin Laden's lieutenants to provide the guerrillas with training on explosives and weapons handling in past years.
About 1,000 Americans spent six months in the southern Philippines earlier this year in counterterrorism exercises aimed at helping the Philippine military fight the Abu Sayyaf.