Pakistani authorities have breached a strategic dyke in flood-affected Punjab to ease pressure on flood defences downstream and protect urban areas.
More than 700,000 villagers have been forced to flee their homes.
Much of the water is reaching Pakistan from Indian-administered Kashmir where flood levels are now falling.
There have been chaotic scenes at one of the region's main airports, Srinagar, as tourists and migrant workers struggle to leave.
The death toll in the two countries has passed 450, with troops deployed to rescue people and provide assistance.
The flooding is the worst Indian-administered Kashmir has seen in decades. Officials say 400,000 people are stranded there and at least 200 people have died.
Pakistan has not experienced floods as devastating since 2010 - officials say 254 people have died in the past few days.
The BBC's Andrew North, near Jhang in Pakistan's Punjab province, says the authorities are struggling to cope with the still growing flood around the city, with thousands more displaced.
At the scene: Andrew North, BBC News, Jhang
Parts of Jhang are now flooded as well as the surrounding area. Many people are taking refuge on dykes with their belongings piled around and their livestock tethered nearby.
Some used tractors to escape the rising waters, carrying rope beds, blankets and feed for the animals. They have now improvised shelters on the dykes.
Rescue teams are still going out on boats to find stranded people. But the relief effort is patchy. Teams of volunteers - some from Islamic groups - have been distributing food, water and medicines, but there's only limited co-ordination and many displaced people say they have not yet received any help.
Some of the new flooding has been caused by authorities breaching dykes to relieve the pressure - that means more villages being inundated.
On Wednesday, emergency teams blew up a dyke on the west bank of the Chenab river upstream from a major dam at Trimmu, in order to prevent flood waters from bursting through. Officials said 200 villages in the area had been flooded as a result.
Floods caused by monsoon rains are an annual event in South Asia and a series of dams on major rivers are aimed at protecting urban areas in particular from being hit by floods. One of Pakistan's largest cities Multan is downstream from Trimmu dam.
Punjab has been taking the brunt of the rain and flooding in Pakistan in recent days. At least 24 people were killed and seven others injured when the roof of a mosque collapsed on Tuesday after days of heavy rain in the city of Lahore, officials said.
Pakistani Prime Minister Nawaz Sharif said the floods were a "sad moment" for the country.
"No-one knew that such a large flood was coming," he told flood victims in Hafiz district on Tuesday.
Across the border, in Indian-administered Kashmir, thousands of stranded people have taken shelter on rooftops of their homes.
Although heavy rains have eased in the Kashmir valley, water levels in Dal Lake in Srinagar are reported to be rising and inundating neighbouring areas.
Using helicopters, boats and naval commandos, troops say they have retrieved more than 76,500 people in flood-affected areas of Kashmir.
Officials said a shortage of rescue boats and lack of telecommunication links - which went down on Monday - were affecting rescue operations.
At the scene: Sanjoy Majumder, BBC News, Srinagar
Hundreds of people are trying to leave Srinagar, the main city of Indian-administered Kashmir.
Hordes of tourists are trying to take flights out of the city's airport, while many migrant workers, who have no money to pay for tickets, are looking for free flights.
Although the rains have subsided, many areas of the city are still water-logged, including neighbourhoods around the Dal Lake.
Pick-up trucks packed with young men are going around neighbourhoods to rescue trapped people as many complain that the authorities are not doing enough.
The main road to the city from the airport is still under water.
Reproduced under licence from BBC News © 2014 BBC