The bad weather stopped his official plane from taking off to fly over the worst hit San Borja region, about 1,000 kilometers (600 miles) northeast of La Paz. Morales has only been in office five days.
The president ordered state help for 800 families who are stranded or have lost their homes in the region. Another 3,600 families have been affected in the Cochabamba, Santa Cruz, Pando and Tarija provinces, according to Defence Minister Walker San Miguel.
At least 50 people have been killed in floods and accidents blamed on the rainstorms over the past week.
On Wednesday, a bus fell into a river near the town of Caranavie and 26 people were reported killed.
La Paz, the capital, has also suffered widespread flooding.