Some 100,000 evacuees, some sleeping outdoors or in their cars, endured chilly weather and another large aftershock overnight that hit the southern island of Kyushu, near the city of Kumamoto.
Several soldiers carried the body down on a plastic tray covered with an olive-green tarp. Dozens of rescue workers continued to dig through the site where a mudslide is believed to have buried several people.
Two other bodies were found late yesterday. At least one appeared to be among the nine reported missing near the town of Minamiaso, according to Japanese media reports. The official death toll stood at 44, awaiting confirmation of the latest death.
After daybreak, Japanese broadcaster NHK showed people squatting at the curbside outside an evacuation center to brush their teeth with water from a green garden hose.
The temperature was forecast to rise to 23 degrees Celsius (73 degrees Fahrenheit) during the day, but fall to 8 degrees (46 F) tonight.
Food and water shortages are plaguing the recovery effort, even as the search for the missing goes on in Minamiaso.
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.
Limited flights also resumed to Kumamoto Airport today, but outbound passenger flights remain suspended because the terminal building is too damaged to handle security checks.
Nine people died in the first, magnitude 6.4 earthquake on Thursday night, and at least 36 in the second quake early Saturday morning, which registered 7.1. Authorities said about 1,100 were injured.
An aftershock with magnitude 5.8 hit the area Monday evening but no further injuries were reported.
Minamiaso, a town of 12,000, was partly cut off by landslides and road and bridge damage. Residents marked their location with chairs aligned in a giant "SOS" while awaiting the US relief flights, which also delivered tents and portable toilets and waste treatment kits.
The flights by two MV-22 Ospreys were a gesture of cooperation between the two allies and a chance for the US military to demonstrate the utility of the tilt-rotor aircraft, whose deployment has raised controversy in Japan due to safety concerns.
The US has about 50,000 troops stationed in Japan, and the American military played a large role in rescue and relief in 2011 after a massive earthquake and tsunami hit the northeastern coast of the main island of Honshu.