Thai troops on Sunday reinforced vulnerable barriers along Bangkok's Chao Phraya river after a sudden rise in the water level set back efforts to contain the worst floods in decades.

Prime Minister Yingluck Shinawatra has warned it could take six weeks for the deadly flooding to recede, telling residents in the capital to prepare for possible inundation up to one metre (three feet) deep.

Three months of heavy monsoon rains have killed more than 350 people in Thailand and damaged the homes and livelihoods of nine million people.

More than 110,000 evacuees have been forced to seek refuge in 1,743 shelters from waters that the government has described as unstoppable.

The authorities are battling the slowly advancing floods on several fronts, with parts of the northern outskirts of Bangkok already under waist-deep water.

Now the level of the Chao Phraya river is causing ‘great concern’, the government said in a statement.

Saturday's overflow caused flooding in relatively small areas of five central Bangkok districts, including near the political heartland prompting a race to fix the leaks before the next high tide on Sunday evening.

The Bangkok authorities urged about 3,000 people living on the banks of the Chao Phraya on the river side of the flood barriers to move to emergency shelters.

In the north of the city, meanwhile, the floods were closing in Bangkok's second-largest airport, Don Mueang, part of which has been turned into a refuge for thousands of evacuees and is protected by walls of sandbags.

More than 150 schools in the capital have also been prepared as emergency shelters.

The government is desperately trying to drain billions of cubic metres of water from upcountry out to sea through rivers and canals in and around the city by opening all sluice gates.

Another major test is expected between October 28 and 30 when seasonal high tides flow up the Chao Phraya, meeting run-off water from the north.

More than 1,000 people have been evacuated from their homes in the northern Bangkok districts of Don Mueang and Lak Si because of overflow from canals in the area.

"But the situation seems to be under control as we see less water overflowing and the military is working to stop the leaks," Don Mueang district chief Phumpat Damrongkiatisak told the media.

Supermarkets in the city have been busy with people stocking up on food and bottled water, while many motorists have moved their cars to the upper levels of multi-storey carparks or left them on bridges and elevated roads.

Tens of thousands of soldiers and police have been mobilised to maintain order and the military has airlifted about a dozen critically ill patients from Bangkok to the eastern province of Chonburi as a precaution.

Aid organisations were also gearing up to assist the city's residents, said Maureen Birmingham, World Health Organization representative to Thailand.

"Bangkok faces the same needs as for other flooded areas but in a far higher quantity," she said, noting the capital was highly dependent on supply chains that might be interrupted.

UN agencies "are aware that there may be a big need for survival commodities."

The government's flood relief centre said that floodwater in Pathum Thani province, just north of Bangkok, had been found to contain toxic chemicals and pollution experts were investigating the cause.

The disaster has dealt a heavy blow to Thailand's export-dependent economy, with hundreds of factories outside the capital flooded.

Most of Thailand's top tourist destinations as well as the capital's main airport have so far been unaffected.