A police official told AFP that a search operation for the 43 missing people was under way, but he saw little chance of finding any of them alive.
Three Ukrainian tourists trekking in the area are among the missing.
At least 13 people died when the floods surged down the Seti river on Saturday.
“We have a list of another 43 people who have gone missing. Their chances of survival are almost zero. The three Ukrainians are still missing,” district police superintendent Sailesh Thapa told AFP.
Earlier reports said the three missing foreigners were Russians.
Fast-flowing floodwaters from the swollen Seti smashed into two buildings and a number of shacks in the village of Kharapani, in Kaski district.
One local woman said she was collecting fire when the flood hit. “We haven’t seen such a flash flood in years,” she said.
“I saw floods 60 years ago but it was not as severe as now. This time they say everything across the river has been swept away.”
The floodwaters also swept into Pokhara, Nepal’s second biggest city, where several people were swept away along with their houses and livestock.
May is the end of the trekking season, but before the monsoon.
The floods are thought to have been caused by waters of the Seti building near its source, high above the snowline, during days of rain and then suddenly bursting free, army spokesman Ramindra Chhetri told AFP.