Flash floods have also washed away hundreds of homes, forcing thousands of residents to flee the area.
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 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.
"There's nothing left for them to survive. People don't even have drinking water," he added. "They urgently need water, food items, blankets and tents."
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 homes.
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, said. "We are still looking for other victims of this flood."
RA/MB