Ben Malor, a spokesman for the UN, said they hoped to resume flights soon but were waiting for the Pakistani military to investigate the incidents in the region of Leepa, southeast of Muzaffarabad, the capital of Pakistani Kashmir.
The incidents happened on Thursday and Friday, after the helicopters had dropped off supplies and personnel.
Malor said: "A group of people decided to hitch a ride. That is not the way we operate."
About 20 people who refused to get off the aircraft were flown to Muzaffarabad, he said.
Helicopters have been crucial in the huge relief effort to help survivors of the 8 October quake, which killed more than 73,000 people in the Pakistani Himalayas.
With some roads swept away and blocked by landslides, helicopters have been the only way of getting help to many survivors in remote settlements.
Malor said all other air operations were going on as scheduled apart from flights to the one area.
Pakistani authorities and international aid agencies have been preparing for an exodus of people from high-altitude areas down to the valleys now that winter has set in, but officials say there has been no sign of a movement of large numbers.
Malor said the people who stormed the helicopters did not appear to be in particularly dire circumstances."They did not look like people who were sick and needed to rush out," he said.