The MI-17 transport helicopter was returning to base late on Saturday after dropping off relief workers in the town of Bagh and all those killed were military personnel, said army spokesman Major-General Shaukat Sultan.
The cause of the crash was suspected to be either bad weather or a technical malfunction, he said.
Bagh is one of the areas worst hit by the 8 October massive 7.6-magnitude quake, and relief workers have not been able to provide enough temporary shelters for residents, let alone for the refugees who have come from the mountains seeking aid.
Only 18,000 tents have been distributed in the region, Pakistani Prime Minister Shaukat Aziz said on Saturday.
The country's relief commissioner, Major-General Farooq Ahmad Khan, said earlier that 100,000 were needed.
Compounding the problem, many people whose houses survived have refused to go back inside, afraid that aftershocks will bring down the weakened structures.
"My house is full of cracks, and I won't go inside," said Mumtaz Rathore, huddled under a plastic sheet with his wife and four children.
Survivors fear aftershocks will
destroy weakened buildings
"Look at me, I have to live out here with my children."
As the rain poured down, soldiers scrambled to cover supplies that had been dropped off by helicopters in previous days. None was flying on Sunday.
"The medicines are the most important thing for us," said Major Ali Agha, directing the effort to save the supplies.
The president, General Pervez Musharraf, said on Saturday that the toll from the earthquake had risen sharply to 38,000, with 62,000 others injured, and warned that the numbers could jump higher as relief teams reached more villages in the endless folds of the Himalayan mountains.
The official death toll has risen
to over 39,000
"There are rescue operations going on, but after eight days it's going to be a miracle" to save anyone else, Musharraf said.
But on Sunday, Pakistani military Major General Farooq Ahmed Khan said at a news conference that the confirmed casualty toll from the earthquake was 39,422 and 65,038 injured.
The number was expected to rise as relief teams discover more bodies under the rubble.
Temperatures were down to 7 Celsius in hard-hit Balakot, where high winds drove the rain, making the town a rain-soaked nightmare for victims, and snow fell in nearby mountains.
Mohammed Qassim, 25, took shelter from the rain under the corrugated roof of a collapsed building.
He was searching desperately for a tent to keep his five children, as well as the families of his two brothers, reasonably warm.
"For the sake of God, please give me one tent so that three families can live," he recalled telling aid groups, most of which appear to have run out of tents. "They said no." He's hoping to at least get plastic sheets.
"We distributed 1000 tents yesterday, but we have run out," said Farhi Butt, who partly owns a telecommunication company that had rushed aid to Balakot.
"For the sake of God, please give me one tent so that three families can live"
Survivor Mohammed Qassim
He had resorted to cutting up plastic signs and distributing them in sheets.
"They're waterproof," he said. "It's not what they're made for, but it will help the people survive for right now."
Aziz made it clear that shelter was now the priority.
"We need tents, tents, tents and prefab housing," he told reporters.
Prime Minister Shaukat Aziz: We
need tents and prefab housing
He also said officials were planning an international donors' conference next week in Geneva.
He estimated that rebuilding Pakistan would cost "close to $5 billion".
While UN officials have estimated the reconstruction would take 10 years, "we think it would be faster", Aziz said.
Pakistan's Interior Ministry on Saturday ordered that visas be granted free to all relief workers and doctors coming to help for the next three months.
Already 2873 emergency personnel from 61 countries have come, the ministry said.
The UN's World Food Programme said it had flown in 35 tonnes of high-energy bars, donated by Norway, to be distributed in the affected areas.
The rations contain enough nutrients for one week for more than 75,000 people, and more flights were planned for next week, the agency said.
Unicef: Thousands of children
could die of cold and disease
Unicef has warned that thousands of children could die from cold, malnutrition and disease.
Overnight rains also prevented troops from getting relief to the three villages still cut off in the Indian-administered portion of the divided Kashmir region, where about 1350 people have died, officials said.
Indian army soldiers on foot were trying to reach Taad, Shararat and Vayu - all at least 10,000 feet up in the Himalayas - said V V Vyas, a top provincial official overseeing relief work.