Pakistan facing 'serious' threat of epidemic disease
Yousuf Raza Gilani was speaking during high-level talks aimed at preventing a mass health crisis.
Doctors in many areas are reportedly struggling to cope with the spread of diseases such as diarrhoea and cholera.
The UN says more than 17 million people have been affected by the floods, with about 1.2 million homes destroyed.
There are fears of further flooding as the Indus river at Hyderabad, already at a 50-year high, is expected to rise even more.
Mr Gilani told the meeting of senior doctors, health ministry officials, UN representatives and members of non-governmental organisations that Pakistan was experiencing "the worst natural calamity of its history".
"As human misery continues to mount, we are seriously concerned with spread of epidemic diseases," he said.
"There is likelihood of water-borne diseases such as cholera, diarrhoea and dysentery, especially in children who are already weak and vulnerable."
Pakistan's national health co-ordinator said the immediate health situation in the flood zone was under control but the threat had not passed.
"Health problems usually arise in flood-affected areas after four to six weeks, and we need to be alert and prepared to tackle the situation," Dr Jahanzeb Orakza said.
The BBC's Jill McGivering in Islamabad says the health meeting appears to be an attempt by the government to improve its co-ordination amid growing criticism about its handling of this crisis.
Doctors in some flood-hit regions are overwhelmed by health problems including skin rashes, dehydration and diarrhoea, says our correspondent.
The flooding has already killed nearly 1,600 people, but millions are considered to be at risk from water-borne diseases, Kazinform refers to BBC News.