An earthquake that struck the southern Philippines left at least 45 people injured, most of them shoppers who panicked and rushed in a stampede for the exits, the civil defence office said Saturday.

The 5.9-magnitude earthquake, located off the southern island of Dinagat, shook nearby areas but caused no major damage or deaths when it struck on Friday, the civil defence agency said.

"Most of them were injured during the stampede at Gaisano Mall. They panicked and they all ran during the quake," said Wilmer Fabella, the agency's administrative officer.

Most of those injured suffered mere abrasions and wounds but at least five suffered more serious injuries and had to be hospitalised, he added.

About 3,000 people were in the newly-opened Gaisano Mall in Surigao City, a mining city near Dinagat Island, when the quake struck.

The government volcanology institute originally classified the quake as 5.7 in magnitude but later raised it to 5.9.

Last month, a 6.7-magnitude earthquake in the central Philippines triggered landslides that left over a hundred people dead or missing.

The Philippines sits on the Pacific Ring of Fire -- a belt around the Pacific Ocean dotted by active volcanoes and unstable ocean trenches.

One fault line runs directly under Manila, a metropolis of more than 12 million people, and government seismologists have warned the city is unprepared for a major quake.