Eight people were pulled from the rubble of a partially collapsed shopping mall near the city of Kumamoto that was torn apart by an apparent explosion about an hour after Tuesday's earthquake. Of them, three have died.

Mall operator Aeon 8267.T said four workers at the Kumamoto shopping centre remained unaccounted for after checks of the roughly 2,700 staff. Customers had been evacuated right after the initial quake.

"Even now, there are people waiting to be rescued, and this is a race against time. We will marshal all available resources on the ground to save and rescue as many people as possible," Prime Minister Sanae Takaichi told reporters in Tokyo.

Authorities are investigating a possible gas explosion at the Aeon mall, media reported. Rescuers reported smelling gas inside the building but the cause of the incident was still under investigation, Japan's top government spokesperson Minoru Kihara said.

Emergency fire rescue teams, police and around 170 army personnel were focusing on areas of the building where calls for help had been received. More than 4,500 soldiers have been deployed to help with recovery efforts across the quake zone.

Seven people are also missing after a chimney collapsed at a Nippon Paper Industries 3836.T factory, while four others are seriously injured, a local government official said. Hospitals were reported to be treating dozens of patients.

Across the prefecture, which also suffered a deadly earthquake a decade ago, around 260,000 people were instructed to go to evacuation centres, authorities said. Police said they received 386 emergency calls after the quake hit, including reports of collapsed buildings and people seeking rescue.