The National Disaster Management Authority (NDMA) said "major peaks" were expected on Friday and next week in Punjab and Sindh provinces.
The region's worst flooding in 80 years has affected 14 million people and killed 1,600, according to the UN.
Doctors say that malaria, diarrhoea and gastroenteritis are growing threats.
On Friday, President Asif Ali Zardari said he would go ahead with a visit to Russia next week, but would stay only a few hours instead of the scheduled two days. It comes after he was heavily criticised for failing to cut short a visit to Europe last week, amid his country's worsening crisis.
Meanwhile, Pakistan's PM has promised aid distribution will be transparent, after criticism of the government's handling of the two-week-old crisis.
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