Floods have swept through nine Thai provinces and eight states in neighbouring Malaysia for a second successive year, prompting both countries to evacuate nearly 45,000 people.
In Indonesia, eight to 13 people are estimated dead following floods and landslides this week, while one has died in Malaysia.
In Thailand's hardest-hit city of Hat Yai, a public health official said helicopters would deliver food and ferry out patients on Wednesday after the first floor of the main government hospital treating 600, some 50 of them in intensive care, was inundated.
"Today, all intensive care patients will be transported out of Hat Yai Hospital," the ministry official, Somrerk Chungsaman, told Reuters.
About 20 helicopters and 200 boats drafted into the Hat Yai rescue effort had had difficulty reaching stranded people, government spokesman Siripong Angkasakulkiat told reporters.
Patients, relatives and medical staff at the hospital number about 2000 and boats should be able to carry in food as the waters recede, Somrerk said.
On a single day last week Hat Yai received 335 millimetres of rain, for its highest such tally in 300 years.
Military helicopters were also carrying generators to the hospital, the Thai Navy said, posting photographs on social media of equipment being moved to a rooftop under dark-grey skies.
Floods across nine Thai provinces, including Songkhla, where Hat Yai is located, have affected more than 980,000 homes and more than 2.7 million people, the interior ministry said.
Thai weather officials forecast scattered thundershowers and heavy rain on Wednesday in several southern provinces, including Songkhla.
Convoys of aircraft and trucks were moving flat-bottomed boats and rubber dinghies towards Hat Yai, along with medical supplies and personnel, said the Thai military, which took charge of relief efforts on Tuesday.
Thailand's only aircraft carrier, Chakri Naruebet, set out from its home port on Tuesday to provide air support, medical assistance and meals in the relief efforts, the navy said.
Rescuers pulled stranded families, including children and the elderly, from homes inundated by swirling brown waters, photographs posted by the Thai army showed.
