Thousands of houses have been destroyed and several villages submerged after flooding triggered by torrential rainfall killed 100 people across Sudan, officials and an AFP photographer said on Sunday.

Thousands of people in the impoverished eastern state of Kasala bordering Eritrea fled their homes after the river Gash burst its banks, flooding entire villages inhabited by farmers.

Many people sheltered in makeshift grass huts on hilltops, after floodwaters also cut off the main highway between east Sudan and the capital Khartoum.

Villagers braved waist-high water as they looked for food, drinking water and medicines amid a shortage of supplies, the AFP photographer said as he toured two flood-hit villages near the provincial capital Kasala.

Many people, mostly children, were seen drinking muddy rain water.

"We had no time. We simply fled, taking our children when our village was flooded in the night two weeks ago," said Taha Mahmoud, chief of Makli village in Kasala.

"We lost all our food, belongings and livestock. We're living in miserable conditions in makeshift huts that won't withstand heavy rains."

"We are eating just one meal a day. Children are falling sick, and doctors are miles away."

Twenty-five people died in Kasala itself and around 8,000 houses have been destroyed since the heavy rains lashed the state two weeks ago, the Sudanese Red Crescent Society said on Sunday.

At least 100 people were killed nationwide, it said.

United Nations aid agencies had warned of flooding in Sudan between July and November this year.

The most affected states are Kassala, Sennar, South Kordofan, West Kordofan and North Darfur, the UN Office for the Coordination of Humanitarian Affairs (OCHA) said on Wednesday.

It said heavy flooding since early June has affected more than 122,000 people and destroyed over 13,000 houses in many parts of Sudan.

A downpour in August 2013 was the worst to hit Khartoum in 25 years, and affected tens of thousands of people, the UN said.

Those floods killed about 50 people, mostly in the capital.