The Meteorological Department said scattered rain was expected for the next two to three days. Bad weather prevented helicopters from ferrying aid to hundreds of thousands of flood-stricken people after a cyclone lashed Balochistan coastline, officials said.
Relief officials said around 250,000 people had been left homeless and at least 21 killed by Cyclone Yemyin, which hit the area on Tuesday just days after thunderstorms left around 230 people dead in the southern port city of Karachi.
"The rain is continuing and has badly affected our relief efforts. Planes and helicopters are standing on runways awaiting clear weather," Khuda Bakhsh Baloch told AFP.
A military statement said 10 army helicopters were on standby to carry out rescue operations as soon as the weather permitted. It was the second successive day that the rain and wind had kept them grounded.
A C-130 Hercules transport aircraft carrying relief goods was also on standby at Chaklala airbase near Islamabad to fly to Balochistan, again subject to the weather clearing, it added. Pakistani troops had evacuated some 4,500 people from some of the worst hit areas along the coast, the statement said.
Baloch said that Balochistan's rail and road links had been damaged by flooding. Gas and electricity supplies to most parts of the province were also cut after a main pipeline and power cables were washed away.
Cyclone Yemyin is the second major storm of the north Indian Ocean cyclone season after Cyclone Gonu hit Oman, Iran and south-western Pakistan in early June, killing more than 60 people.
The United Nations said on Wednesday that the destruction in Pakistan - plus floods in neighbouring India and extreme weather across Europe - showed the world must be better prepared to cope with the impact of climate change.
Military joined efforts to help up to 900,000 people affected by a cyclone as more rain exacerbated flooding and hampered airborne rescue and relief operations. Severe weather at the onset of the South Asian rainy season has killed about 400 people in Pakistan and India over recent days and more than 40 people have been killed in floods in Afghanistan.
The cyclone and subsequent flooding in Balochistan have killed 25 people, while 12 people were killed on Thursday in a separate deluge in the north-west of the country. Rising water levels in Balochistan inundated a fourth district - Sibi - on Thursday. Three others were severely flooded, said the relief commissioner.
"Due to torrential rain a seasonal river has started overflowing and 20 to 25 villages have been inundated. According to our estimates about 15,000 people have been affected," Baloch said. Troops had evacuated more than 600 families from Turbat, which was "surrounded by water from all directions," the statement said, and another 300 from nearby Bela. Soldiers also provided relief goods and security to passengers on a train stuck for two nights in Balochistan after the rain washed away tracks.
A navy helicopter rescued 40 people marooned on a rooftop near Turbat and two other choppers were evacuating car and bus passengers from the coastal highway, which was partly washed away by storm surges, the statement said.
Three army C-130 Hercules aircraft carrying relief goods landed at Turbat and a nearby town, along with a navy plane with medicines and other emergency supplies.
But the military said the situation at a swollen dam near Turbat was still "critical" with water above the danger level, adding that a battalion of engineers was working to shore up the site. The floods have washed away stretches of road and several bridges, and cut communications and power supplies. Floods also severed a gas pipeline, cutting supplies to the provincial capital, Quetta.
Rail and road links had also been damaged by flooding. Illustrating the conditions facing rescuers, Minister for Communications Shamim Siddiqui was caught in heavy rain while trying to reach the affected area in a helicopter and was forced back to Karachi, the state news agency said.
Troops had rescued hundreds of marooned families while the navy had rescued two seamen - a Mexican and an Indian - who had been adrift at sea for three days, it said. Torrential rains also lashed North West Frontier Province killing at least 16 people, most of them Afghan refugees, in the rugged tribal belt bordering Afghanistan, officials said.
Eight refugees were buried when their mud-brick house collapsed in Landikotal, the main town in the district and the last before the famous Khyber Pass border crossing, a local administration official said.
Three other refugees were swept away and killed when a bridge on the Peshawar-Kabul highway near the town collapsed due to the rain and sent their truck plummeting into a canal. Two local women and a child were drowned in a rain-swollen river in Landikotal while a couple was reported killed in a house collapse in the town, he said on condition of anonymity.