Flooding has forced more than 4,000 people from their homes in the town of Cobija in northern Bolivia after the river Acre burst its banks.
Heavy rains have also caused the nearby river Tahuamanu to burst its banks.
Vice-President Alvaro Garcia Linera travelled to Cobija on Tuesday to deliver aid to the town.
He said some of the neighbourhoods located closest to the river would have to be moved and promised government help to relocate their residents.
The mayor of San Pedro de Bolpebra, on the border with Peru and Brazil, said his town had been almost completely swept away by floodwaters.
"The river waters rose to 14m [46ft] above their normal level, so between the community and the authorities we have decided to rebuild a new town to avoid more damage," Mayor Romulo Terrazas said.
Cobija resident Jhenny Huasimave told La Razon newspaper that she had lost "almost everything" and was staying in a shelter in a local sports centre.
"We're looking after the little we have left and are sleeping in the stands," she said.
"But our situation is a sad one, it's too crowded, we need help," she added.
Vice-President Garcia said the government would send more help in the coming hours.
Bolivia's Amazon lowland plains are subject to flooding every year during the January-March rainy season, but the flooding this year is some of the worst, meteorologists say.