At least 13 people were killed when a 6.8 magnitude earthquake struck southern Japan on Tuesday, injuring hundreds and knocking out power and water to tens of thousands.

The revised death toll was announced by the prime minister, Sanae Takaichi, on Wednesday morning after the quake, which registered a maximum 7 on the Japanese shindo intensity scale, struck Kumamoto prefecture on the southern Kyushu island.

Rescue crews were sifting through the wreckage at key sites, including that of a paper mill in Yatsushiro where a chimney collapsed. Two workers were found and taken to hospital in a state of cardiac arrest, with nine others missing.

An explosion was reported in an Aeon shopping mall, which houses around 200 outlets, in the prefecture shortly after the earthquake and footage appeared to show the upper section of the main building torn away and partially collapsed. Two women in their 20s were confirmed dead, and another person reportedly suffered cardiac arrest.

An Aeon spokesperson said customers and employees were evacuated after the initial quake and the cause of the explosion remained unclear. A government official told reporters that Aeon Kumamoto reported a gas leak, though the cause had not yet been determined.

The Japanese military mobilised 3,600 personnel for disaster relief operations and sent 20 aircraft to assess the damage from the air, the defence minister said. Hundreds of first responders from neighbouring prefectures arrived in the affected areas on Tuesday evening.

The Japan Meteorological Agency (JMA) warned that areas with the biggest tremors would remain at risk of further strong quakes and landslides for about a week because the shallow earthquake was triggering seismic activity in the area.

By Wednesday morning more than 60 aftershocks had been recorded, ranging in magnitude from 1 to 4, the agency said. A tsunami warning was issued immediately after the quake, ​but was lifted within two hours.

Nearly 50,000 households were without power late on Tuesday, along with 140,000 without water. Temperatures in the region were forecast to top 30C on Wednesday, with high humidity increasing the chance of heatstroke for those without access to air conditioning and water. Large numbers of people slept in their cars overnight out of fear of aftershocks.

Despite the earthquake’s intensity, relatively few buildings collapsed, reducing the number of fatalities and injuries. Japan has strict construction standards and earthquake resistance requirements for new buildings have been raised multiple times over recent decades. Technology such as apartment blocks with foundations laid on rollers that can sway means newer structures are able to withstand intense shaking.

Takaichi said on Tuesday evening that authorities were still assessing the extent of the damage in the area, which was devastated by another deadly quake a decade ago.

“We have already been informed that people have been injured. Power outages and fires have occurred in some areas, and there has also been damage to roads and bridges and the collapse of buildings,” Takaichi said. “I ask everyone to take action to protect themselves, including evacuating to a safe location.”

By Wednesday morning, five houses had been confirmed collapsed. More than 350 people had been treated at local hospitals, many of which were affected by power and water outages and damage to medical equipment.

“People are coming in with burns and fractures from being trapped under objects due to the earthquake, and ambulances are constantly bringing in injured people,” NHK quoted one hospital employee as saying. “Inside the hospital there are water leaks and electrical system failures.”

About 300,000 people were instructed to go to evacuation centres, the disaster management agency said.

​JR Kyushu, the regional railway company, suspended services on Tuesday, including its high-speed bullet trains. Kumamoto airport also shut its runway as airlines diverted and ​cancelled flights.

Telecoms operators KDDI and NTT Docomo ‌said there was disruption to their ​mobile phone services owing to power shortages ​and transmission-line failures. There were no irregularities reported at the nuclear power stations in the area, Japan’s nuclear regulation authority said.

Footage from NHK on Tuesday showed multiple buildings on fire or partly collapsed, along with large fissures on ‌major roads, including an elevated highway. TSMC, the world’s largest contract chip maker, Sony and Fujifilm evacuated workers from their factories in the area.

Chiharu Hara, a 35-year-old recruitment agent who was in Kumamoto, told AFP that she was “terrified” when the quake struck. “The office swayed violently side to side. I was afraid it would collapse. Everyone panicked,” Hara said.

The quake’s epicentre was about 12 miles (20km) south of Kumamoto, central Kyushu island’s largest city, with a population of about 700,000. The US Geological Survey initially said the earthquake had a magnitude of 7.1, but revised it later to 6.8. The JMA said it had a magnitude of 7.1 but reached the highest level of 7 on Japan’s own shindo scale. A subsequent aftershock with a magnitude of 6.1 was registered at 5.08pm.

The Geospatial Information Authority of Japan reported that the Earth’s crust had moved 84cm in Yatsushiro city, where the paper mill is located, and up to 40cm in Kumamoto city.

Japan, which is located along the “ring of fire” of volcanoes and oceanic trenches in the Pacific basin, is one of the world’s most earthquake-prone countries, with a tremor occurring at least every five minutes. The country accounts for about 20% of the world’s earthquakes of magnitude 6 or higher.

An earthquake in Kumamoto 10 years ago killed 275 people and injured a further 2,739. It damaged thousands of buildings including the city’s castle, a popular tourist site. Some of the castle’s stone walls were damaged in the latest quake. Two days before that earthquake, a powerful foreshock struck nearby.

Japan is haunted by the memory of a massive 9.0-magnitude undersea quake in 2011, which triggered a tsunami that left around 18,500 people dead or missing and wrecked the Fukushima nuclear plant.