An earthquake with a preliminary magnitude of 5.8 hit the Kumamoto prefecture in southern Japan on Monday, the Japan Meteorological Agency said.
Broadcaster NHK said a tsunami warning had not been issued.
Two deadly quakes hit the same region last week, killing 42 and injuring more than 1,000.
Japan on Monday enlisted US help to airlift supplies to some of the 100,000 people made homeless by earthquakes in the country’s south, as rescuers struggled to find those still missing in a massive landslide.
Many of those evacuated after their homes were damaged or destroyed have been forced to sleep in temporary accommodation or huddle in makeshift shelters, and media have reported problems in delivering food and other emergency supplies.
The disaster-prone country’s worst humanitarian challenge since 2011 - when a quake, tsunami and then nuclear meltdown hit the northeast coast - has left 42 dead and more than 1,000 injured.
Prime Minister Shinzo Abe said the government was working to find survivors and care for the displaced, and that the US military had sent aircraft to help with the daunting relief effort.
“Many people are spending anxiety-filled days at evacuation facilities,” he told reporters. “We will continue to offer hands-on assistance to the individuals affected.”
Around 10,000 people are staying in their cars at an exhibition hall parking lot in the town of Mashiki, but emergency supplies have not been delivered as the facility is not registered as a shelter, Fuji television said.
In another case, volunteers sent supplies and the military brought six tons of water to a hospital in Kumamoto city after a doctor complained on Facebook that there was not enough water or food for patients.
“Thanks to this, we don’t have to worry about water to wash hands after treating patients,” doctor Takeshi Hasuda said.
Kumamoto’s mayor took to Twitter today to apologise to the “many voices” who had complained about delays in providing help.
“Please be patient,” Kazufumi Onishi wrote, promising that the situation would quickly improve.
The twin quake disaster comes at a particularly sensitive for Abe, just months ahead of elections for the upper house of parliament.
Up to 25,000 Japanese military and other personnel have fanned out through villages where scores of traditional houses have been left in ruins by Saturday’s 7.0 magnitude quake, which struck a part of Japan not used to such tremors.
Nine people are still missing, feared engulfed by landslides, after earthquakes struck the island of Kyushu.
An initial quake on Thursday, measured at 6.2 magnitude by US geologists, affected older buildings and killed nine people. But Saturday’s more powerful tremor brought even newer structures crashing down.