The toll in Surobi District included many women and children, officials said Saturday.
Allah Mohammad, a member of the provincial council, said numbers are likely to rise from the current 96 confirmed dead.
The National Disaster Management Authority said flooding has also been reported in Nangarhar and Kunar provinces, Khaama Press said. There were no reports available of casualties in those areas.
The flooding has damaged farmland and destroyed crops.
Surobi, the capital of the district, is about 40 miles from Kabul in Kabul Province.