Eleven more were killed in across other areas of Afghanistan while avalanches in neighbouring Pakistan killed at least 23 people on Saturday night.
Rescue workers are struggling to find 15 more people missing in Turkoh, a remote village in the Hindu Kush mountains in the Chitral region.
Hundreds of cattle were also killed by the rains as the floods inundated thousands of hectares of land and washed away or damaged bridges around the country, including in the capital, Kabul.
Rains also caused avalanches and landslides in northeast Afghanistan, where nearly 20 people died last week.
Meanwhile, three children were killed when a suicide bomber blew himself up near a convoy of soldiers in eastern Afghanistan, a provincial police spokesman said.
Three soldiers and four other civilians were also wounded in the attack in the province of Laghman, around 100km east of Kabul.
The explosion occurred near a base that is believed to be run by US troops.
The Nato-led International Security Assistance Force confirmed there had been an incident, but gave no details.
Seven policemen were killed in a Taliban ambush on Saturday as they were travelling to support another unit being attacked in the district of Shorabak in the southwest of the country.
The ambush took place on Saturday as the reinforcements headed to a post in Shorabak district in the southwestern corner of the country.