Patients, relatives and medical staff at the hospital number around 2,000 and boats should be able to carry in food as the waters recede, Somrerk said.
On a single day last week, Hat Yai received 335mm of rain, 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 over 2.7 million people, the interior ministry said.
Thai weather officials forecast scattered thundershowers and heavy rains 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.
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