The death toll from flash floods in northern Afghanistan rose to more than 100 on Saturday with many others still missing, officials said, as helicopters carried trapped villagers to safety.

The national disaster management authority told AFP that 58 people were killed in Jowzjan province, 32 in Faryab, six in Sar-e-Pul and six others in Badghis as floods struck a large swath of rural communities.

OCHA, the United Nations humanitarian affairs office, said it had reports from provincial officials of 123 people killed, with Jowzjan province alone suffering 80 deaths and 6,000 displaced people.

It said clean water, medical supplies, food and shelter were needed immediately as relief efforts got under way after days of torrential rain.

The floodwaters swept through villages, engulfing thousands of homes and leaving many people seeking safety on the roofs of their mud-brick houses.

"Unfortunately, we have over 100 people killed and dozens of others missing due to flash floods in four northern provinces," Mohammad Sadeq Sediqqi, of the national disaster management authority, told AFP.

The Afghan defence ministry sent two helicopters to Jowzjan, where the aircraft rescued more than 1,000 people and carried them to higher ground.

Officials in Faryab province said nearly 2,000 houses were washed away and more than 8,000 cattle were killed by the floods.

Authorities said food and other emergency supplies were being distributed, as well as cash hand-outs.

President Hamid Karzai in a statement said he was deeply saddened by the loss of life and property, and ordered relief work to be stepped up.

Flooding often occurs during the spring rainy season in northern Afghanistan, with flimsy mud houses offering little protection against rising water levels.

Two weeks ago, a landslide triggered by heavy rains and a small earthquake swept through two villages in the northern province of Takhar, killing four people and destroying around 100 houses.

In the last major flooding in Afghanistan, 40 people died in August in flash floods in eastern and southeastern provinces and some districts of the capital Kabul.