Meteorologists said that some 100 millimetres (four inches) of rain had fallen per square metre -- seven times more than had been forecast the day before.
The high-alert was triggered chiefly by conditions in Ostrava, the main town in the northern Moravia region, where the Ostravice river burst its banks during the day and flooded surrounding streets.
The flooding, which also affected the towns of Bohumin, Havirov and Cesky Tesin, threatened to spread towards neighbouring Poland, according to meteorologists.
"We are advising people to move into the higher floors of their houses and to be ready for an evacuation," the mayor of Bohumin, Petr Vicha, said.
Conditions in the southwest of the Czech Republic near the border with Austria, however, improved Wednesday, as the flooding experienced in previous days began to subside.