The floods hit Parwan, Kapisa, Panjshir, Maidan Wardak, Logar, Paktia, Paktika, Nuristan, Nangarhar, Laghman, Khost and Ghazni provinces, reports TOLO News.
The worst-hit province of Parwan has so far reported 93 deaths and 110 injured.
According to government statistics, 1,500 houses were damaged in these provinces.
Afghanistan's Meteorological Department has forecast more rains in Nangarhar, Kabul and the Wakhan area of northern Badakhshan province in the next 24 hours.
The government has said that relief efforts were also underway.
Floods were also reported in Nuristan in the east and Logar province in the past 24 hours but there was no information about casualties and damages.