The flooding, hitting provinces mainly in the north and center of the country, had caused serious damage to around 900 houses, killed hundreds of cattle and damaged agricultural land, Hashmat Khan Bahaduri, spokesman for the Afghanistan Natural Disaster Management Authority (ANDMA), said, Reuters reported.
Officials were assessing damage, he said.
The floods, which came after an unusually dry winter that has led to drought in many areas, underline Afghanistan's vulnerability to natural disasters.
The rugged mountainous terrain and the lack of roads mean it is often difficult to evaluate relief needs but ANDMA had sufficient resources to deal with the problem for now, Bahaduri said.