The central city of Durazno is the most affected, with 5,299 evacuees, according to official reports.
Defense Minister Jose Bayardi visited one of the camp sites managed by the military to help the displaced.
"We have established a high level of experience (in the face of these catastrophes) which we have succeeded in institutionalizing," he told the media.
Military troops will continue monitoring the situation because "there are many people who do not want to leave their homes due to fear of being robbed," Bayardi said.
The National Highway Police also said that 12 national routes remain cutoff in different directions.
Uruguay's National Meteorological Institute said that between June 11 and 16, some southern regions of the country received around 270 mm of rain.
On Wednesday morning, the Yi River, which had been 11.8 meters higher than its normal water level in the Durazno area, was falling at a rate of 11 cm per hour, according to local media reports.
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