Sixteen people have been killed in central Zambezia province since heavy rains sparked the floods last weekend, said Maria Luciano from the National Institute of Disaster Management.
The figure could be even higher, because there was no information from all the areas that had been cut off, she added.
A total of 200,000 people were estimated to have been affected in the province, where helicopters were dropping food to isolated areas.
South Africa sent a team of soldiers and health workers to Zambezia to help with the rescue effort.
Further up north, the flooding hit Niassa province, where 18 people were killed, Radio Mocambique reported.
Trains no longer circulated between Niassa and neighbouring Malawi, where floods have killed 48 people.
Rescuers salvaged more than 800 people in Nsanje and Chikwawa districts in the south, Malawian Vice President Saul Chilima said, adding that rising water levels were preventing army helicopters from reaching some areas.