The organisation said Thursday most of the children have had little food and safe drinking water since the beginning of the disaster.
A further 11,220 victims are pregnant women, of whom 3,400 are expected to deliver within the next three months.
In most parts, the organisation said populations are still without safe drinking water, health care and other basic services, bringing the fear of epidemics.
As a result, it set up a team of four experts in the areas of public health, epidemiology, malaria, nutrition and sanitary engineering, following appeals by the Mozambican government.
The team has since been working in close collaboration with other agencies in providing technical support to the government for dispensing emergency relief.
Health minister Francisco Songane, accompanied by the organisation's representative and senior officers from his ministry, visited some affected areas in Maputo province.
They confirmed the health situation was very grim. In certain places, people have been living in very precarious conditions, even sleeping under trees.
"There are many people suffering from lack of food, shelter and any kind of medical assistance," the organisation said.
Sanitation was also lacking and could significantly increase the risk of epidemics.
There has already been a cholera outbreak in some regions, with an average of between 15 and 18 confirmed cases being reported every day.
"Outbreaks of vaccine-preventable diseases such as measles and meningitis are also a major threat to which an immediate response is needed," the organisation said.
But compounding the problem is the lack of sufficient health facilities, some of which have been damaged and others isolated by the floods.
"Health services in the affected areas are overwhelmed by the number of patients and are working beyond capacity. Drug stocks are running out and there is a serious shortage of health workers," the organisation added.
The health ministry is reviewing the situation with the possibility of reassigning staff from non-affected areas and recruit new ones.
A rapid assessment of the flooding is, however, yet to be carried out in six provinces of Maputo City, Maputo, Gaza, and Inhambane in the south, and to a lesser extent the central provinces of Sofala and Manica.
And because most roads have been damaged, the only suitable means of distributing food, medicines and other goods is by light aircraft and helicopters - which significantly increase operational and transport costs.
Up to now, only 50 percent of the available food has been distributed due to damaged roads and most of the needs of the affected population remain unmet.
Observers say this situation could worsen as the rains continue, with the virtual isolation of some flooded areas.
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