Another 36 people were injured in the floods, agency spokesman Janan Sayaq said.
Officials previously reported 33 deaths nationwide.
Sayaq added that the floods caused significant damage, including destroying agricultural land and homes.
Afghanistan is reeling from the after-effects of decades of conflict and one natural disaster after another, including floods and earthquakes. A series of earthquakes in the Western province of Herat in October claimed at least 1,500 lives, according to the UN.
In February, an avalanche struck a mountain village in Nuristan province, killing at least 21 people.
The lack of robust infrastructure, particularly in remote areas, often exacerbates the consequences of such disasters.