Twenty-one people were killed in flooding in the south-western district of Surkhet, according to Kantipur Television. At least 44 were missing.
Seven people were killed when a swollen river swept them away in Dang district, also in south-western Nepal.
In nearby Bardiya district, five were dead and 15 were missing in floods. Four people were killed in floods in Banke district.
Sixteen people were reported killed by landslides in several districts.
The torrential rains obstructed major highways and stranded hundreds, while hundreds more have been displaced by flooding in the southern plains.
The Home Ministry said dozens of people were expected to be missing, but no precise figures were available yet.
A total of 156 people were missing after a landslide in the central district of Sindupalchowk last month, with 33 confirmed dead.
The Sunkoshi River remains blocked by the natural dam and heavy rainfall has triggered fear that it might burst its banks.