Heavy rain along with melting snow has caused mud slides in the Mures region, the ministry said. Hundreds of homes and thousands of acres of farmland have been inundated by flood waters.
Disaster crews have been evacuating people for two days from the affected villages, according to a Mures official, Cristian Vladu.
"The police were able Sunday to save three shepherds and some 400 sheep that were stranded since Saturday on a small island in the region," Vladu said.
About ten Romanian regions still remain on alert as the weather forecast calls for more rain next week.