Thailand has started pumping water from the Mekong River into its own waterways, sparking concern from downstream countries like Vietnam, which is suffering its worst drought in almost a century.

Key points: Thailand approves future giant pumping station

Thailand approves future giant pumping station Vietnam says Mekong is at lowest level since 1926

Vietnam says Mekong is at lowest level since 1926 South-East Asian countries desperately need water

The Mekong River runs through China's Yunnan province, Burma, Laos, Thailand, Cambodia and Vietnam. ( Supplied: Wikipedia )

Four temporary pumps have begun sucking 47 million cubic metres of water out of the Mekong River and into the Huai Luang River, in Thailand's Nong Khai province.

"These pumping stations are only temporary to help assist people during the drought crisis," said Dr Somkiat Prajamwong, from Thailand's Royal Irrigation Department.

The Huai Luang project is relatively small scale, but Thailand's National Water Resources Board has approved a much bigger pumping station for the area that could divert 150 cubic metres every second from the Mekong River.

The Royal Irrigation Department said work on the giant pumping station was unlikely to begin for two years, and insisted it would abide by regional agreements on managing the Mekong waterway.

"We hear that Vietnam sent the message to the Thailand [but] they probably misunderstand our status… the water that we take is not [a] significant impact," Dr Somkiat said.

Thailand, like the rest of South-East Asia, desperately needs water.

Things are so bad at the Ubolrat dam in northern Thailand that they are about to dip into the so-called "dead storage".

That is the dregs of a reservoir that sit lower than the bottom of the pumps — in this case the last 1 per cent.

Water levels in the Ubolrat dam are so low Thailand will soon be using the last 1 per cent of "dead storage". ( ABC: Liam Cochrane )

Farmers like Auchalin Konkong welcomed the Huai Luang pumps.

Sorry, this video has expired Mekong River diverted into Thailand's waterways ( South-East Asia correspondent Liam Cochrane )

"We usually have to set up the pump and pump water for so many days before it is enough for rice farming, [but] if we get help from this project we don't have to pump water so far," Ms Auchalin said.

Locals said these mega-projects have been talked about for many years but have been fast-tracked by Thailand's military junta, which took power in 2014.

"Under the military government, they seem to listen to information from bureaucrats rather than villagers or other people," said Santiparp Siriwattanapaiboon, a scientist from Rajabhat Udon Thani University.

Soldiers have been mobilised to help dig 4,300 wells and build new 30 new "monkey cheek" dams — named after the primate's habit of storing food in its cheek for later consumption.

Mekong at lowest level in 90 years

While Thailand continues to block rivers feeding the Mekong and divert small volumes, Vietnam said it had recorded the lowest levels of the Mekong River since 1926.

Salinity in the Mekong Delta is a growing problem for Vietnam's rice bowl and has been made worse by rising sea levels pushing salty water upstream.

Modelling conducted by the Mekong River Commission predicted salt intrusion on Vietnam's main Mekong channel would reach up to 162 kilometres inland this year, which is nearing the Cambodian border.

A normal year would see salt intruding only 98 kilometres inland.

Thailand is hoping the rainy season comes in late May, but the current El Nino weather pattern has so far exceeded forecasts — meaning South-East Asia's water resources and regional relations could be further tested.