Shoppers and merchants fled the scene in panic after the explosion on Sunday and police cordoned off the area.
"It could be a bomb," one policeman at the scene said. "We're waiting for the experts."
"The earth shook," one dazed woman said. "It was a loud explosion."
Three people died at the scene and 10 in three different hospitals, Chief Superintendent Antonio Billiones, the region's police chief, said.
"We are still investigating to determine the type and make of the explosive device used in the attack," he said.
While the mayor of General Santos said the blast could have been caused by feuding merchants, police noted recent reports of threats by Muslim rebels from Abu Sayyaf, a homegrown group.
Billiones said the police had been receiving intelligence reports, as early as September, on alleged plans by the Abu Sayyaf to bomb the city.
"I don't want to speculate, at this point, on any group that could be behind the attack because there are so many rebel groups operating in the city," the police officer said.
It was unclear if the blast was
the work of rebel groups
"It's too premature to pin the blame on any particular group at this time."
City mayor Pedro Acharon dismissed talk that the attack was the handiwork of rebel groups, saying he had received reports that two groups of stall owners were fighting for control of the public market.
"We have been on alert because we learned about a plan to burn the market four days ago," he said. "This will hurt the city's efforts to attract investors and tourists."