The US military said the CH-47 Chinook was flying near Chakothi when the incident occurred at 1345 local time.
However, Pakistan said it believed the firing was mistaken for dynamiting taking place to clear landslides.
It said the incident would not affect US relief operations. The US has more than 20 helicopters delivering aid.
Pakistan says 57,000 people were killed in the 8 October earthquake and three million made homeless.