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The death toll from devastating flash floods in northern Afghanistan has risen to 153 people across three provinces, the Taliban's interior ministry said on Saturday.

At least 138 people have also been injured in the flooding across northern Baghlan, Takhar and Badakhshan, caused by heavy rains on Friday, ministry spokesman Abdul Mateen Qaniee told Reuters.

Taliban authorities sent helicopters to try to assist civilians overnight after receiving reports that over 100 people were stranded.

Many people had been left homeless and transportation, water and waste systems were "severely disrupted", according to the World Health Organisation (WHO).

"The impact has been profound, leading to loss of life and injuries, with many individuals still unaccounted for," the WHO's Afghanistan office said in a statement late on Friday.

It added that four health centres had been damaged and one destroyed by the floods and said the agency was sending health teams to provide treatment in the inundated areas.

Flash floods caused by heavy rains have devastated villages in northern Afghanistan, killing 315 people and injuring more than 1,600, authorities said on Sunday, as villagers buried their dead and aid agencies warned of widening havoc.

Thousands of homes were damaged and livestock wiped out, the Taliban-run refugee ministry said, while aid groups warned of damage to health care facilities and vital infrastructure, such as water supply, with streets left coated in mud.

In the Nahrin district of Baghlan province, people carried their shrouded dead to a gravesite.

"We have no food, no drinking water, no shelter, no blankets, nothing at all, floods have destroyed everything," said Muhammad Yahqoob, who has lost 13 members of his family, children among them.

The survivors were struggling to cope, he added.

"Out of 42 houses, only two or three remain, it has destroyed the entire valley."