"From Friday onward, because of the rains there were flash floods which caused high human and financial losses," department spokesman Janan Sayeq said.
"The primary information shows that, unfortunately, in the floods, 33 people were martyred and 27 people got injured."
Most casualties were from roof collapses while some 600 houses were damaged or destroyed, nearly 600 kilometres (370 miles) of road demolished, and around 2,000 acres of farmland "flooded away", Sayeq said.
Some 20 of the nation's 34 provinces were lashed by the heavy rains, which have followed an unusually dry winter season which has parched terrain and forced farmers to delay planting.
Since the Taliban returned to power in 2021 the flow of foreign aid into the impoverished country has drastically diminished, hindering relief responses to natural disasters.
At least 25 people were killed in a landslide after massive snowfall in eastern Afghanistan in February, whilst around 60 were killed in a three-week spate of precipitation ending in March.
The United Nations last year warned "Afghanistan is experiencing major swings in extreme weather conditions".
Scientists say harsh weather patterns are being spurred by climate change and after being ravaged by four decades of war Afghanistan ranks among the nations least prepared to face the phenomenon.
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