Days of devastating flooding across Southeast Asia have killed more than 250 people across Indonesia, Thailand and Malaysia, authorities said on Friday.

Heavy monsoon season rains paired with a tropical storm system inundated areas across the three countries, stranding residents on roof tops and cutting off entire communities.

The tolls in Indonesia and Thailand rank among the highest in flooding events in the countries in recent years

In Indonesia, authorities were struggling to reach worst-affected areas on Sumatra island while authorities at a southern Thailand hospital brought in refrigerated trucks to store bodies after the morgue exceeded capacity.

Officials on Sumatra said flooding and landslides this week have killed at least 111 people, with nearly 100 more missing.

More rain is forecast for much of Sumatra, though the intensity is expected to ease, officials said.

Among the hardest-hit areas in the region is southern Thailand, where flooding left residents of Hat Yai clinging to rooftops awaiting rescue by boat.

At least 145 people have been killed across the country's southern provinces, government spokesman Siripong Angkasakulkiat said on Friday, as receding floodwaters allowed a clearer picture of the disaster.

Most of those are concentrated in Songkhla province, where authorities at the Songklanagarind Hospital said they had no more room to receive bodies and were now relying on refrigerated trucks.

In Malaysia, two people have been killed in flooding caused by heavy rain that left stretches of northern Perlis state under water.

Over in Sri Lanka, authorities deployed the military for relief and rescue operations on Friday as the death toll from floods and landslides rose to 56, with another 21 people listed as missing.

Helicopters, navy boats and armoured personnel carriers are being used to evacuate marooned villagers in several parts of the country, the Disaster Management Centre said, as the rain continued.

The island's entire 65,000-square-kilometre area is experiencing rainfall, with some regions seeing 360 millimetres in the past 24 hours, the centre said. (AFP)