The Paraguay river has reached a height of 9.64m (32ft) in Alberdi in Neembucu province, and officials have warned that flood defences are about to burst.
But Neembucu's governor said locals had refused to follow advice to leave.
The El Nino weather phenomenon has triggered some of the worst floods seen in 50 years in the region.
Dyke experts suggested as early as Saturday that resident should be evacuated.
National Emergency chief Joaquin Roa warned that a breach of the defences was imminent and would almost certainly lead to loss of life.
Neembucu Governor Carlos Silva said that people "do not want to believe they real danger they are in".
While the village itself is not yet flooded it has been cut off by the rising waters of the river Paraguay.
The army is helping villagers to cross the river Paraguay by boat to the Argentine city of Formosa.
From there, they are flown by military plane to the Paraguayan capital, Asuncion.
Residents of a village in south-eastern Paraguay are refusing to leave their homes even though flooding is imminent, officials say.