A magnitude 7.1 earthquake struck southern Kumamoto prefecture on Japan's Kyushu island at 4.27pm local time on Tuesday, the Japan Meteorological Agency reported, at a depth of about 10 kilometres. The United States Geological Survey measured the same event at magnitude 6.8.

The JMA issued a tsunami advisory for the Ariake and Yatsushiro seas, forecasting waves of up to one metre, and ordered coastal residents to move away from the water. The advisory was lifted within about two hours. A magnitude 6.1 aftershock followed at 5.08pm, and the agency told residents to expect further aftershocks for about a week and warned of landslide risk on saturated slopes.

Local authorities issued level five emergency safety orders covering 92,743 people across two municipalities and level four evacuation orders covering 78,628 people across five more. More than 40,000 households lost power. JR Kyushu suspended rail services across the island, including shinkansen, without setting a resumption time. No irregularities were reported at nuclear plants in the region.

The most serious damage was at an Aeon Mall in the town of Kashima, where the second floor gave way. The local fire service said the collapse may have followed an explosion, caused by a gas leak after gas equipment was damaged in the shaking. Six people had been pulled out by Tuesday night, according to local officials, one of them in what emergency services described as cardiopulmonary arrest and five with injuries that were not life-threatening.

The number of people still inside is not settled. NHK, citing local officials, reported about 10 people unaccounted for. Other outlets, citing the fire service, put the figure at between 20 and 30 mall employees. AFP reported at least one person killed. AUNS has not independently verified any casualty figure and none of these counts has been confirmed by a national authority.

About 80 people were being treated at the Yatsushiro Northern Regional Medical Center in Hikawa on Tuesday night, and about 10 more were hurt at a nursing home in the same town. Officials logged 12 collapsed houses, four separate incidents of people trapped in buildings, two fires and 13 other rescue call-outs.

The outer walls of Kumamoto Castle came down again in clouds of dust. The castle has been under restoration since the 2016 Kumamoto earthquakes, which killed 275 people and injured 2,739.

Takuya Nishimura, a professor at Kyoto University, said the two events are linked. "It is highly likely this earthquake resulted from remaining fault movement from the 2016 quake's southern section," he said.

What held on Tuesday is as much of the story as what did not. Japan's earthquake early warning system pushed alerts across seven prefectures before the shaking arrived. The tsunami advisory went out and was withdrawn on the observed data rather than left running. The reactors stayed within tolerance. A shopping centre floor did not, and that is what rescue crews were working on overnight.

Rescue operations at the Kashima site were continuing on Wednesday morning Australian time. The JMA has not downgraded its aftershock advisory.