"The Mekong floods have caused an alarming number of child fatalities, most of them due to drowning," it said in a statement, announcing it was stepping up its response to the disaster.
Jean Dupraz of the UN Children's Fund in Vietnam said preventing drowning was the agency's priority.
"Populations here have lived along the Mekong River for centuries. Still many children do not know how to swim. And it takes only a few minutes for a child to be swallowed by powerful river streams," he said.
UN agencies, along with Save the Children, have provided a total of more than 9,000 floating school bags and 3,200 life vests to help protect children from drowning.
More than half a million people have seen their homes or livelihoods affected by the rising waters, which have inundated around 140,000 homes.
Unusually heavy monsoon rains have caused devastation across the Mekong region, with more than 500 dead in Thailand's worst flooding in half a century and around 250 killed in Cambodia.