Narathiwat Governor Thanon Vejjakornkanont said all 12 districts have been inundated, with almost 30,000 people affected, but only eight were declared disaster zones.
Eighteen schools in Ra-ngae district have been forced to close.
The eight Narathiwat districts are Yi-ngo, Bacho, Rangae, Sungai Kolok, Waeng, Chanae, Cho-I-Rong and Tak Bai.
Meanwhile, Pattani Disaster Prevention and Mitigation Office chief Panyasak Sophonvasu said 790 families have been affected by the flood. The Pattani River overflowed in three districts—Paka Harang, Baraho and Talubo—with water 100-150 cm deep, and is still rising.
The Pattani River rose after a sluice gate was opened allowing flood water from Yala to flow into the province.
Although the rain has eased, the earlier heavy downpour in the province and in Yala has brought more water into the Pattani River.
The province has prepared shelters for flood victims.
In Nakhon Si Thammarat, the Taloompuk peninsula was further pounded by strong waves as high as four metres which kept slamming the shoreline. Seawater inundated villages and many coconut trees were felled.
Some villagers evacuated after local authorities cut electricity and water mains as a safety precaution and to protect public utilities which could be damaged by the flood.
In Songkhla, the municipality posted signs warning tourists not to swim at Samila Beach, the province’s major tourist attraction, because of strong wind and high waves which damaged the shoreline for 300 metres.
The provincial disaster prevention and mitigation office reported that four districts were hit by flood which caused more than Bt8 million in damage.
Department of Disaster Prevention and Mitigation Director-General Wiboon Sanguanpong said heavy rain continued in the southern provinces, particularly on the east.
Heavy rain has triggered flooding in six provinces -- Phatthalung, Surat Thani, Nakhon Si Thammarat, Yala, Songkhla and Narathiwat.
The Meteorological Department warned of heavy rain and strong wind and high waves in the South.
In its latest announcement, issued at 4.30pm, the department said the strong northeast monsoon remains over the south and the Gulf of Thailand, causing scattered to fairly widespread thundershowers and isolated heavy rainfall on the east coast from Surat Thani southward.
People in at risk areas along foothills, near waterways and in lowlands are warned of flash floods.
The at-risk areas included Nakhon Si Thammarat, Phatthalung, Songkhla, Pattani, Yala, Narathiwat, Trang and Satun.
Strong wind and high waves in the lower Gulf of Thailand from Nakhon Si Thammarat southward are expected at 2-3 metres high.
Shipping should proceed with caution and small boats are advised to stay ashore.