Thailand put its military in charge of tackling a devastating flood crisis on Tuesday and readied reinforcements to evacuate thousands of people, as heavy rain hobbled relief efforts after some of the worst flooding to hit the south in years.

Floodwaters running as high as 2 metres in some areas have struck nine southern provinces and killed 13 people in Thailand, while eight states in neighbouring Malaysia were inundated.

Thailand's military flew in a C-130 cargo plane with supplies of medicine, food and water, and the navy said a flotilla of 14 boats and the aircraft carrier Chakri Naruebet would depart later on Tuesday with two helicopters, doctors and field kitchens that can supply 3,000 meals a day.

"The fleet is ready to deliver forces and carry out actions as the Royal Navy orders," the military said in a statement, adding the carrier could also serve as a floating hospital.

Operations have been focused largely on the southern commercial hub Hat Yai, a centre for Thailand's rubber trade and its fifth-largest city.

Its provincial governor said boats, high-clearance trucks and even jet skis were being used to evacuate residents.

Hat Yai received 335mm of rain on Friday, its highest in a single day for three centuries.

"Calls have been coming in non-stop in the last three days, in the thousands, asking to be evacuated and others for food," said a member of a volunteer group, the Matchima Rescue Center in Hat Yai.

An estimated 2.1 million people have been affected in Thailand, with 13,000 moved to shelters and many others cut off and unable to get help.

In Malaysia, more than 19,000 people have been moved from flooded areas to 126 evacuation centres set up mainly in northern border areas.

The floods could wreak disruption in Thailand's rubber industry, among the world's largest producers and exporters of the commodity. (Reuters)