Air New Zealand confirmed the cancellation and apologised to customers for the inconvenience.
Customers were being offered accommodation and would be rebooked on the next available service.
Earlier, National Business Review owner Todd Scott tweeted that the flight had been diverted to Guam before the decision was made to return to Auckland.
"Eng issue means they have to descend. Altitude at 15,000 feet, so likely a pressurisation problem," he tweeted.
But an airline spokeswoman said NZ99 was always scheduled to operate via Guam for a fuel stop, but turned back because of a problem with the onboard air reticulation system.
"The decision was taken to return to Auckland rather than carry on to Guam once the problem became known," she said.
"Secondly, there was no engine issue. The problem was with the onboard air reticulation system (air con if you like). Nothing to do with the engines.
"Thirdly, there was no pressurisation issue. This was simply an issue with air reticulation, not pressure.
"Finally, there was no emergency. The aircraft simply returned to Auckland. Engineers are now fixing the problem and the aircraft is expected to be back in service later today.
"Air NZ will now work to re-accommodate the 256 passengers on board the flight on alternative services in order to get them to their destinations. We sincerely apologise to customers for this inconvenience."
Nine of Air NZ's 11 Dreamliner aircraft have been undergoing checks because of potential problems in Rolls-Royce Trent 1000 engines, and the airline announced today that it will remove two of the planes for service in Singapore.
Repairs are expected to take several months because maintenance facilities are busy with other Dreamliner aircraft with the same engine fault.
