Provincial spokesmen in Nangarhar, Kabul, Khost, and Nuristan said on Sunday that all the floods had occurred early Saturday.
Flash floods are common in all those provinces.
In Kabul's Surobi district, police chief Shaghasi Ahmadi said 13 people were killed and up to 50 were missing in a remote and mountainous area.
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Surobi has a number of rivers running through it. It is also rife with Taliban activity.
Downstream in the adjacent province of Nangarhar, an announcement said 17 people were killed by the floods.
President Hamid Karzai's office said another seven died in Khost and Nuristan.
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