The WHO and UNICEF have warned that diseases such as malaria, cholera, leptospirosis, dengue fever, dehydration, diarrhoea, gastroenteritis and skin infections will have a telling effect on the region.
Food, drinking water and medicines are being distributed, but the scale of the disaster has dwarfed relief efforts.
"Entire villages are days away from a health crisis, if people are not reached in the coming days," said UNICEF's health chief in India, Marzio Babille.
Children, who make up 40 percent of South Asia's population, were particularly vulnerable, he said.
India is the worst affected country, with some 20 million people in the states of Assam, Bihar and Uttar Pradesh hit by the floods, according to the UN.
Some eight million people are affected in Bangladesh and another 300,000 people in southern Nepal, the UN said.
Although water levels are receding in Nepal and Bangladesh, millions of people are still marooned on high ground. Most water sources in affected areas are either contaminated or submerged, a BBC report said.
Babille was quoted as saying that an acute shortage of helicopters meant that Indian authorities in India were finding it difficult to reach victims, who have spent more than a week in the open, after their houses were either washed away or surrounded by water.
There has been a brief pause in the rain but reports indicate more rain is on the way and the flood season is likely to continue for several weeks.
Union Home Minister Shivraj Patil and Congress party head Sonia Gandhi visited parts of flood-hit Assam and Bihar on Tuesday, where the flood-hit expressed their frustration over not receiving adequate government attention in terms of aid.
The UN said that in Bihar alone, more helicopters are needed for rescue and relief operations. Floods in the state have affected nearly seven million people.