The floods in the remote mountainous district of Baghlan province come a month after a landslide triggered by heavy rains buried a village and killed 300 people in a nearby region.
The twin disasters highlight the challenges facing underdeveloped Afghanistan's next leader as the country heads into the second round of the presidential election on June 14.
"People have lost everything they had - houses, property, villages, agricultural fields, cattle," Baghlan police spokesman Jawed Basharat said about the floods.
Afghan disaster management officials said they were scrambling to get food and medical aid to the area after torrential rains unleashed the floods, which forced thousands of people to flee their houses.
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Officials recovered 58 bodies from the inundated areas, including women and children, with several people said to be missing, according to the National Disaster Management Authority (NDMA).
"There is a lot of stagnant water, and there are more bodies under the rubble and mud," Mohammad Nasim Kohzad, head of NDMA in Baghlan, told AFP. "We are still looking for other victims of this flood."
"The floods destroyed four villages, and washed away 2,000 residential houses, agricultural fields and also killed thousands of cattle," the governor of Guzargah-e-Nur, Noor Mohammad Guzar, told AFP.
Officials were further assessing the extent of the damage on life and property in the affected area, the deputy head of the National Disaster Management Authority said.
"Our teams have also provided some edibles (food items) and medication to the affected people. More aid will get there soon," said Mohammad Aslam Sayas.
Last month a landslide triggered by heavy rains buried a village in a remote area of northeast Badakhshan province killing at least 300 people.