Many in the quake zone whose homes were not seriously damaged sought shelter as the area was rocked by more than 500 aftershocks.
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Hundreds of people have been sleeping in their cars.
Japanese media reported that a 51-year-old woman from Kumamoto had died on Monday from the condition.
At least 23 people have developed symptoms, Kyodo News service said.
With 180,000 people seeking shelter, some evacuees said that food distribution was a meager two rice balls for dinner. The Fire and Disaster Management Agency said almost 1,200 houses had been destroyed.
The Japanese Meteorological Agency (JMA) is continuing to monitor activity from the volcano, and has maintained its alert level at 2.
The country has suffered widespread damage after recent earthquakes-the first natural disaster measured a magnitude of 6.5, while the second was even stronger with a magnitude of 7.0. There, dozens of troops, police and other rescue workers were shoveling debris and searching through places where they may have been buried.
Temperatures around Kumamoto city are forecast to fall to 8C (46F) overnight.
Disruptions from damage to buildings and roads, and from outages of electricity and water supplies, were reverberating beyond Kyushu as manufacturers suspended output.
US airlifts delivered water, bread, ready-to-eat food and other emergency supplies to the remote area of southern Japan stricken by the two powerful earthquakes.
A girl helps her mother, background, to collect water at Aso Shrine in Aso, Kumamoto prefecture, Japan Tuesday, April 19, 2016. “But so far the road access is not easy to the remote areas”. “We have already seen of several of the mid to upper 5 plus magnitude range, and over the next several days and weeks, we would not be surprised to see more earthquakes of this size”, said John Bellini, a geophysicist with the US Geological Survey (USGS).
Meanwhile, Kumamoto airport reopened Tuesday, allowing the first flight carrying passengers and relief goods to land for the victims.
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Officials said that the death toll from the quakes rose to 46 as two more bodies were recovered, while the number of missing remained at eight as the bodies had yet to be identified. Students of Tokai University are briefed before boarding a helicopter for evacuation in Minamiaso, Kumamoto prefecture, Japan, Saturday, April 16, 2016.
