Van Langenhove said: "The end is not yet in sight.
"The Cuvelai area is a disaster, the floods are at the highest level we have seen in over 35 years," he said, referring to an area in Angola north of the Namibian town of Oshakati.
Rescue officials have begun evacuating schoolchildren in some areas by boat across the rising Zambezi river into Zambia, and from there, by road back to Namibia.
Fatal night flights
The river normally reaches its highest levels towards April, but is currently at record highs, Van Langenhove said.
Heavy rain in Angola washed away roads and bridges and forced the closure of scores of schools in the north.
Most of the victims were children or the elderly who drowned when crossing floodplains during the night.
Gabriel Kangowa, head of the emergency management unit of Namibia, said: "We have had lots of drownings at night, when people can't see where they are going."
The UN Children's Fund last month said that about 150,000 children in southern African were in need of humanitarian assistance because of floods.
At least 45 people have died in Mozambique, Zambia, Zimbabwe and Malawi since torrential rains swept through southern Africa in December and January.
The subsequent floods have swept away livestock and crops, prompting fears of food shortages and outbreaks of disease.