"The forecast weather is outside of the usual forecasting and more extreme than our 12 months of modelling and other data stretching back much further."
To compensate for the extra fuel required to fly into the headwind, and to avoid a stop in Fiji, the airline had to move 15 passengers on to alternative routes leaving today and tomorrow, the spokeswoman said.
"We are grateful to these customers for their assistance and they will receive compensation and hotel accommodation where needed.
"Weather on the eastern seaboard of the United States has caused disrupts to a number of airlines and it is common aviation protocol to reduce customer numbers on flights when weather calls for it.
"We want to thank our customers for their patience and understanding while we work through this exceptional weather pattern."
Earlier this week a flight on the new route was at one stage thought to need a stop in Fiji to refuel due to weather issues.
However, this was avoided after changes to the route while airborne, a spokeswoman said.
The inaugural 787 flight suffered similar issues with strong headwinds and difficult weather, leading the flight to offload passenger luggage and take on additional fuel in order to make the ultra-long route.
The airline - which launched the flagship route last weekend - launched a review in the wake of that incident.