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.

Some 250 people were still cut off by Sunday, the Kyodo news agency said. Collapsed bridges and waterlogged ground on steep hillsides were hampering rescue efforts, according to media.

A total of 20 people have died while more than 20 remain unaccounted for in the Fukuoka and Oita prefectures, Kyodo reported.

The government was doing its "utmost" to recover those missing or stranded, Chief Cabinet Secretary Yoshihide Suga earlier said in a rare weekend press conference.

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.