Swathes of Kyushu -- the southernmost of Japan's four main islands -- have been left devastated after overflowing rivers and torrential downpours swept away roads, houses and schools this week.
Thousands of people have been evacuated to makeshift shelters in school gyms and public buildings, but many remain stranded, with emergency services battling through thick mud and rain to try to reach them.
More than 500 people were still cut off by Sunday, public broadcaster NHK reported, with collapsed bridges and waterlogged ground on steep hillsides hampering rescue efforts.
The government was doing its "utmost" to recover those missing or stranded, Chief Cabinet Secretary Yoshihide Suga said in a rare weekend press conference.
Officials of Fukuoka and Oita prefectures said a total 18 people had been confirmed dead while 27 were missing or could not be reached.
Five people were in critical condition, Suga said, with the government still trying to ascertain if their injuries were a result of the severe weather.
Television footage showed rescue helicopters held up at a makeshift heliport -- unable to fly because of the downpours, while people prayed for the safety of their family members.
More than 50 centimetres (20 inches) of rain deluged parts of Kyushu in 12 hours on Wednesday, prompting the Japan Meteorological Agency to warn of possible significant damage.
Rains have continued intermittently since, with up to 22 centimetres recorded in Fukuoka in the past 72-hour period.
Japan's weather agency on Sunday warned of continued heavy rains and mudslides in northern Kyushu.