Mohammed Amin Fatemi, the Afghan health minister, said the flood waters had damaged nearly 3,500 houses, many of them built from mud bricks, and killed around 2,300 farm animals.
The remoteness of the area, near the town of Balamurghab, about 30km from the border with Turkmenistan, has meant that details of the casualties and damage are difficult to confirm.
The Italian-led International Security and Assitance Force team in the western city Herat was also working with local authorities to assess the damage and line up assistance, spokesman Captain Giancarlo Ciaburro told the AFP news agency.
"There are reports of 100 people dead but we don't know the numbers because the area is not very reachable," he said.
ISAF teams had said Balamurghab was under 10 centimetres of water, he added, warning that there could be health problems later because of rotting animal carcasses in the water.
Afghanistan, especially the west and south, has been in the grip of drought but heavy rains started falling in several areas in the past week.