"Things could get worse as we expect rains to continue until March. We need international aid because we do not have the resources."
The floods have already cost Bolivia up to $500m, newspapers reported on Wednesday.
State television showed people wading in chest-high water in towns in the central province of Cochabamba, where local media said three young sisters had drowned.
The flooding is blamed on the La Nina weather phenomenon in the Pacific Ocean that has exacerbated Bolivia's rainy season.
The local meteorological service forecast that rains will continue for at least another month.
Evo Morales, Bolivia's president, has asked for aid from neighbouring countries to meet the food and medical needs of the more than 32,000 families affected.
Brazil and Chile have sent helicopters to help in rescue efforts.
Alex Contreras, a government spokesman, said Morales had sent all his cabinet ministers to assess flood damage and help victims in various parts of the country.