Aid agencies said entire villages had been washed away in the region’s worst flooding for 80 years.
Unicef said 3m people had been affected and 1,400 had been killed. Other estimates said between 800 and 1,500 had died, with 27,000 still trapped.
Renewed rain on Tuesday slowed the relief effort, with criticism rising of the pace of the government response.
In Swat, where thousands are still rebuilding after a major military operation against Taliban rebels during 2009, the flooding has brought down bridges and left communities cut off.
Adnan Khan, a spokesman for the disaster management authority in the worst-affected province, Khyber-Pakhtoonkhwa, told that logistics were now an immense challenge.
“The entire infrastructure we built in the last 50 years has been destroyed,” he said.
The return of monsoon rains has grounded helicopters and raised fears of renewed flooding.
Just as emergency services and the army said they were making some headway, the rains have come again. That has meant an immediate suspension of helicopter flights that were getting to stranded people.
We’ve had about two hours of very heavy downpours. It has just eased up but more are expected in the coming hours – floodwaters could rise again and rivers will burst their banks again. Aid operations will have to be suspended for even longer.
There are many areas the army admits that it has not reached at all. There are several valleys in the north-west of Pakistan where they do not know how many people have died or how much destruction there is. Time is now crucial for those people waiting for aid, who do not yet have food or clean water.
The army had hoped that the initial rescue operation could be over in 10 days, but says rebuilding the damaged areas could take more than six months.
Khyber Pakhtoonkhwa Information Minister Mian Iftikhar Hussain said rescue teams were trying to reach 27,000 stranded people, including 1,500 tourists in the Swat Valley.
But the biggest challenge for the emergency services is access, as so many areas had their transport and communication links destroyed and are now isolated.
There are also concerns that yet more places could flood: a warning was issued to villages close to the Warsak Dam overnight, but no evacuation order was issued.
The Pakistani military says it has committed 30,000 troops and dozens of helicopters to the relief effort, but winching individuals to safety is a slow process.
Reports say that Islamist groups, some accused of having links to the Taliban, have been providing aid to many of the victims.
Some survivors have complained that the government has responded slowly; several hundred people protested in the city of Peshawar, where homeless survivors have crammed into temporary shelters.
IAid agencies say the risk of water-borne diseases spreading will remain high until the floodwaters fully recede. Mr Hussain, , said there were reports of cholera emerging in the Swat Valley.
Dr Ahmed Farah Shadoul, the World Health Organization’s acting head in Pakistan, told the BBC it was essential to act against the spread of a number of infections, including diarrhoeal diseases, skin problems, eye problems, malaria and fevers, and measles.
The UN children’s agency Unicef said more than a million children needed emergency aid.
Dr Shadoul said he had received reports of people being bitten by snakes, and said the WHO had provided anti-venom in some regions.
Food is scarce in the area and water supplies have been contaminated by the floods.
Unicef says it has been working with the Pakistani authorities to repair wells and provide chlorine tablets so that water can be treated before it is drunk.
“We are also getting confirmation of reports about an outbreak of cholera in some areas of Swat,” he added.
Governments around the world have pledged millions of dollars in aid, but there has been no decision yet on whether to launch a global appeal for aid.