Khyber-Pakhtoonkhwa, formerly named North West Frontier province, has been worst hit but the flooding has also affected the central Pakistani province of Punjab.
Al Jazeera's Sohail Rahman, reporting from the banks of River Swat in northwestern Pakistan, said damaged bridges were making it difficult to reach people stranded by flood waters.
"Nearly three dozen helicopters are being used by the Pakistani military and the international community trying to help those who have been stranded," he said.
"There are thousands of people on each side of the banks trying to get across to safety. The navy has also arrived."
Officials said about 30,000 troops were involved in rescue efforts.
But some residents in the northwest were becoming increasingly angry with what they said was a lack of government response.
"My son drowned," Sehar Ali Shah, a local resident, told Al Jazeera. "The government is not taking care of us. It has not managed to find any alternative place for us to move to."
Hakimullah Khan, a resident of Charsadda town, told the Associated Press news agency that he has not received any help in tracking down his missing wife and three children.
Several camps, offering food and medicine, have been set up in schools and community centres by provincial and relief organisations in Khyber-Pakhtoonkhwa province.
The threat of disease raised concerns as some evacuees arrived in camps with fever, diarrhoea and skin problems.
"Our doctors have treated over 600 people just in the last two days and they are seeing a lot of cases of diarrhoea, fever and skin infections," Sonia Cush, the director of emergency response at Save the Children in Washington, DC, told Al Jazeera.
|Aid agencies warned that waterborne diseases could spread in flooded areas
"We currently have emergency health teams moving around within the affected area treating people who urgently need healthcare, and our priorities are food, clean drinking water, healthcare and hygiene materials to ward off diseases.
"We will be distributing plastic sheeting to build makeshift shelters, but the hard work will only begin once the flood waters start to recede."
Officials from Unicef, the United Nations' children fund, said contaminated flood waters and lack of clean water could increase the risk of the spread of diarrhoeal diseases.
Children under five are especially vulnerable to dehydration from diarrhoea. With more than 40 per cent of the population under 18 years of age, the number of
children affected could be in the hundreds of thousands, they said.
A variety of nations and aid organisations have begun to mobilise a response to the disaster.
The United States announced on Sunday that it would provide Pakistan with $10m in humanitarian assistance.
The floods came after what meteorologists described as an "unprecedented" 30 centimetres of rain fell in just 36 hours. Experts believe the worst of the rainfall is now over, but the extent of the damage is still being assessed.
Poor weather may also have been a factor in Wednesday's Airblue plane crashthat killed 152 people near the capital, Islamabad.