"Dozens of homes were washed away, some with entire families inside, so we still don't know how many people were killed," said Carlos Quesada, director of the National Emergency Commission.
While Cesar lost much of its force and was downgraded to a tropical depression Sunday when it hit Nicaragua, swollen rivers continued to wash away homes rivers and bridges on Sunday night.
The emergency agency said overflowing rivers caused severe flooding in Perez Zeledon, 70 miles south of the Costa Rican capital, where at least 21 people are still missing.
It also reported outbreaks of malaria and cholera as the flooding wiped out drinking water supplies.
The Mexican government issued a storm watch for the Pacific coast from Puerto Madero to Acapulco.
Forecasters warned that Cesar could pick up strength against as it moved west with winds of more than 34 mph with gusts of 46 mph. At 11 p.m. EDT Sunday, it was centered off the coast of El Salvador.
With winds of 80 mph, Cesar killed three people in Colombia on Saturday, lashing the archipelago of San Andres. Eight children were missing in northern Colombia after an avalanche.
The U.S. National Weather Service hurricane center in Miami warned that heavy rains in the Gulf of Fonseca area, where Nicaragua, Guatemala, El Salvador and Honduras meet, could cause mud slides and flash floods.