Up to 8 inches of snow fell in some high-altitude areas and up to 1.2 inches of rain drenched some lower areas, Meteorological Department Chief Qamaruz Zaman said.
"Flights are off for today," said a spokesman for the UN World Food Programme in Muzaffarabad.
An International Committee of the Red Cross (ICRC) official said their air and road operations had also been called off.
"Bad weather stopped flight operations in the affected areas," a spokesman for the army's relief effort in Azad Kashmir, Major Farooq Nasir, told AFP.
"Relief operations by air have been hampered but the ground relief is going on," he said. "Roads are still open and so far there is no information of any landslides causing blockades."
A race against time is on to ensure hundreds of thousands of homeless earthquake survivors are given adequate shelter and enough food to see them through a bitter winter. If not, disease could sweep through cold, poorly nourished survivors, causing a second wave of death, aid officials say.
Qamaruz Zaman said the rain had started on Saturday, and was continuing sporadically in northern Pakistan and parts of Kashmir on Sunday.
Snow was falling in the village of Pieer Chanasi on Sunday afternoon and residents were grim.
People were seen placing plastic sheeting over their tents to keep the rain water out. Inside their tents, men, women and children circled around fires to keep warm.
"We're in trouble. Our children and animals are also in trouble," said Tanvir Naqvi. "The temperature is dropping and a tent is not enough."
Fresh landslides, apparently triggered by the rain, disrupted traffic on the road up to the village, which was under about 2 inches of snow.
The authorities hope people in high-altitude settlements will come down to tent camps on valley floors for the winter, but most people have chosen to stick it out at their ruined homes.
Aid officials are making plans in case bad weather sends a flood of people down into unsanitary and over-crowded tent camps in Muzaffarabad and other towns.
The ICRC official said good weather up to now meant aid deliveries were slightly ahead of schedule, but prolonged bad weather would be a worry.