Ernesto Suarez, Beni's governor, was quoted as saying by the local newspaper, La Prensa: "If this happens, we are going to be in dire straits."
Suarez said about 6,000 people have been evacuated from Trinidad's outskirts and that the worst flooding is yet to come.
"They are saying the hardest blow will come after the 28th (of February). If this happens, Trinidad will be in serious trouble."
Floods have drowned an estimated 22,000 head of cattle in Beni and wiped out about 194,000 hectares (480,000 acres) of farmland in the neighbouring state of Santa Cruz, officials said.
Bolivian officials said there have been an large increase in cases of malaria and dengue.
To date, 1,660 cases of dengue, 1,452 of malaria and 22 of leptospirosis have been recorded, according to a government report.
The UN has issued an international call for $9.2 million in emergency assistance to care for flood victims and fight waterborne diseases.
Evo Morales, the Bolivian president, thanked Venezuela and Peru for sending flood relief, singling out Peru's centre-left government for overlooking recent political disagreements.
"When there are emergencies like this the ideological differences end," Morales said.
"I wish to salute the Peruvian president and people. We'll never forget this."
The US, Italy and Japan also sent relief.
The government says some 350,000 Bolivians are suffering the hardships of extreme weather triggered by El Nino - fluctuating marine-atmospheric systems characterised by warm surface waters in the eastern Pacific, a phenomenon that some scientists say may be aggravated by global warming.