A view of Aeon Mall shopping centre, after an explosion occurred following an earthquake. Photo: Reuters

The death toll rose to 18 by Wednesday evening with at least 62 people injured, including six suffering serious injuries, the prefectural government said.

More than 170 aftershocks have jolted Kyushu, Japan’s southernmost main island, since Tuesday’s earthquake, while nearly 10,000 people have been displaced from their homes and taken to evacuation centres.

One of the largest rescue operations remained focused on the Aeon shopping mall in Kumamoto, where an explosion tore through the building about an hour after the earthquake.

As of Wednesday afternoon the company operating the mall said three people had died in the incident, while another three remained missing. Another eight people had been pulled from the heavily damaged mall in overnight operations.

The mall had only reopened last month after years-long renovations following damage from another major earthquake in 2016, which had including measures to strengthen the building against seismic activity.

The president of the Aeon Mall in Kumamoto, Akio Yoshida, told a press conference search was ongoing to find the remaining people missing. "We take it seriously that an explosion happened and precious lives were lost," Mr Yoshida told the news conference, where he bowed deeply alongside two other executives.

Some 3,000 customers were inside the mall at the time of the earthquake, and between 1,300 and 1,500 employees, according to Mr Yoshida.

Rescue operations continued in nearby Yatsushino, where a chimney collapsed in the intense shaking at a Nippon Paper Industries factory, killing five workers. Seven others were rescued.

Four people were still believed to be trapped there, said the Kumamoto prefectural government disaster team.