"Up to 3.5 million children are at high risk of deadly water-borne diseases including diarrhoea-related, such as watery diarrhoea and dysentery," he said, estimating the total number at risk from such diseases to be around six million.
OCHA said figures for how many people may have already died from disease following the floods were not available, but insisted work was being done to assess the situation.
"The mortality caused by the incidence of these diseases is increasing. We don't have figures at this moment, but WHO is working round the clock in support for the government to come up with numbers," he said.
Patients turned away
Medical teams working on the ground are in no doubt as to the scale of the threat posed by diseases. At the Dera Ismail Khan government hospital in Peshawar on Monday, staff reported being inundated with hundreds of patients suffering from diarrhoea and vomiting.
Many were turned away from the hospital as doctors focused their resources on helping sick children, staff said.
Cholera, which can spread rapidly after floods and other disasters, poses a serious threat, says the UN. The disease has been detected in the northwest, but there have been only a few reported cases so far.
Typhoid and hepatitis outbreaks are also a risk as survivors of the floods, which have killed at least 1,600 people, are forced to drink unclean water to survive.
The health warning comes a day after Ban Ki-moon, the UN secretary-general, said that the disaster was the worst he had ever seen and renewed calls for international aid donations.
The cost of rebuilding Pakistan could exceed $10 to $15 billion, the country's High Commissioner to Britain said on Monday.
"It will take at least five years," High Commissioner Wajid Shamsul Hasan told Reuters in an interview on Monday.
Asked about the cost of rebuilding, he said, "I think more than $10 to $15 billion."
He said this was a rough estimate because an assessment of the extent of the damage caused by the floods had yet to be carried out.
But the number gave an indication of the scale of the reconstruction needed.
The World Bank has said that $1 billion in crops have been lost. On top of that is damage to infrastructure, to schools, hospitals and houses, to dairy farming, and to industry.
"These floods have really dislocated everything," Hasan said.
After the flood waters receded, the World Bank and other institutions would have to assess the damage.
"In the longer term, when the water subsides, we need reconstruction ... We'll have to have a long-term plan, something like the Marshall Plan."
The UN has appealed for an initial $460 million to provide relief, but only 20 per cent of the total has so far been pledged. Officials say that billions more will be needed for reconstruction after flood waters recede.
With more than 20 million people made homeless by the floods, authorities have been overwhelmed by the scale of disaster, and many have been angered by the lack of assistance they have received.
In the hard-hit Sukkur area in southern Sindh province, hundreds of flood victims blocked a major road with stones and rubbish to protest what they described as a slow delivery of aid.
Kalu Mangiani, one of the protesters, said government officials only came to hand out food when media were present.
"They are throwing packets of food to us like we are dogs. They are making people fight for these packets," he said.
Al Jazeera's Imran Khan, reporting from Sukkur, said it was clear that not enough aid was getting to flood victims.
"Without a co-ordinated effort by the government or aid groups, delivering supplies becomes a piecemeal effort that falls short of what is needed," he said.
"The scale of this disaster is overwhelming and the lack of a centralised effort means good intentions can go to waste."