Japan was struggling to send food and water to the southern island of Kyushu on Monday after two powerful earthquakes there killed at least 43 people and forced about 100,000 to leave their homes, local media reported.

Authorities said they were facing challenges in sending relief aid to disaster-hit areas in the prefectures of Kumamoto and Oita, where significant damage to roads, bridges and railways and a shortage of workers made delivery difficult.

In Minamiaso village, where nine people were still unaccounted for, some communities were cut off after the quakes triggered a large-scale landslide and caused a 200-metre-long bridge to plunge into a valley.

Evacuees in some rural areas of Kumamoto have received only limited supplies, the local Nishinihon newspaper reported.

Some residents evacuated to a local school in Nishihara village, east of Kumamoto city, where they said they have received insufficient food aid, according to the report.

"We received only one rice ball and one cup of ice cream," a 25-year-old mother with a baby was quoted as saying.

Some evacuees spent more than two hours lining up for a bottle of water and a rice ball, the report said.

Prime Minister Shinzo Abe told officials during a government meeting Monday that the top priority was to "ensure the delivery of enough food and water to every disaster victim."

Abe also said he was grateful for the support from the United States as the US military delivered emergency supplies to evacuees in rural Kyushu.

Across Kumamoto and Oita prefectures, about 100,000 evacuees remained at schools, gymnasiums and community centres, local government officials said.

More people spent the night in cars as aftershocks continued to jolt the region and some shelters remained overcrowded.

More than 500 aftershocks have jolted Kyushu since the first magnitude-6.5 quake hit Kumamoto on Thursday evening. A magnitude-7.3 earthquake struck the same area early Saturday, according to the Meteorological Agency.

"Seismic activity seems to be calming down, but could conceivably start to intensify again," Gen Aoki, the head of the Meteorological Agency's tsunami and earthquake monitoring section, said at a news conference.

The two major quakes last week prompted the closure of some express ways on Kyushu and the suspension of local train services, including high-speed shinkansen trains that were launched five years ago.

Train operator JR Kyushu was unable to say when it would resume the operation of the high-speed bullet trains, as the quakes damaged a number of elevated tracks, the Nishinihon newspaper reported.

Kumamoto Airport, whose facility has been closed since its ceiling collapsed, will reopen Tuesday, and some airlines will resume their flights, Kyodo News agency reported.

The two major quakes last week were the strongest since the earthquake and resulting tsunami in north-eastern Japan on March 11, 2011, according to the Meteorological Agency.

Those twin natural disasters killed about 18,500 people and triggered Japan's worst atomic accident at the Fukushima Daiichi Nuclear Power Station.

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