Millions of people are living rough and dependent on aid, but the bad weather has shut down relief deliveries by helicopter.
However, officials said that for the time being they were still able to use roads to get food and other supplies to people in remote areas.
The 7.6-magnitude quake killed more than 87,000 people and levelled entire towns and villages, leaving more than 3 million homeless in northwestern Pakistan and Pakistani-controlled Kashmir.
Most survivors are living in tents and other makeshift homes, many of them already suffering from respiratory illnesses, diarrhoea, scabies, tetanus and other ailments.
Survivors and officials had hoped that winter would be a little late this year, providing time to get more aid to the area and make better preparations for the cold weather. The first heavy rain since the quake drenched those hopes.
Shahid Kazmi, a junior government official who has been living in a tent with his wife and two children for weeks, said: "Today's rain has wet our tent, and I wish it had delayed for a few weeks."
He said they could not burn wood in the tent to stay warm.
Survivors struggle to stay warm
in their tents
"We don't know how we are going to survive," he said.
For Raja Mohammed Ali, who owned a shop destroyed by the quake, a comfortable life with his family is only a bitter memory.
"Today we are in a tent," he said, worried about the health of his wife and five children. "I never thought that one day we will live like this."
Thousands of deaths
Aid agencies have said that thousands more deaths could occur during the Himalayan winter if sufficient shelter and food are not made available.
Major Farooq Nasir, a Pakistan army spokesman, said no helicopters could fly in Kashmir on Sunday because of rain and clouds.
"We are using road links to supply food and other essential items to people," Nasir said. He said snow that fell on the outskirts of Muzaffarabad and elsewhere was quickly cleared from roads.