"A part of the blade has come adrift inside the engine and that's what's caused the vibration," he said.
Pilots shut down the engine and, in line with standard procedure, headed for the nearest airport.
A similar problem happened on a Rolls-Royce Trent 1000 engine on a Dreamliner flight to Buenos Aires the next day, hastening the turbine blade replacement programme that has been rolled out around the world since last year.
Older engines fitted to Dreamliners, which first flew commercially in 2011, are affected.
"This is not an Air New Zealand issue this is a worldwide Rolls-Royce fleet issue. It's unfortunate that we've had two of the six incidents that have ocurred around the world. It's unfortunate and coincidental," Morgan said.
About 200 Trent 1000 engines need replacement alloy turbine blades, which are prone to corrosion, and the programme to replace them will stretch into next year.
"The reality is that we were operating the aircraft in accordance with the manufacturer's recommendations, which had a safety buffer built in," Morgan said.
Two planes have been grounded for repairs meaning cancellations and delays this weekend, and these could stretch into weeks.
Read more:
Air NZ Dreamliner Rolls-Royce engine problems cause cancellations
The one-tonne engines have to be flown to a Roll-Royce facility in Singapore. This takes more than a month.
"We feel very comfortable about the safety and operational integrity of the fleet based on the revised maintenance programme advice from Rolls-Royce and the regulator," Morgan said.
Air New Zealand has 11 Dreamliners. Two of its newest planes have new engines, which have been modified and not prone to the problem.
Morgan said the priority now was finding each seats to match demandcoming into the busy peak season.
"It's certainly not helpful - we're very cognisant of the expectations of the travelling public as we're heading into the Christmas peak."
Air New Zealand was approaching other airlines for spare aircraft or capacity.
"Airlines do this from time to time. We've operated services for other airlines when they've had difficulties with fleet and this is a similar situation," he said.
A New Zealand Air Line Pilots' Association (NZALPA) spokeswoman said today that the association's technical specialists were helping the Transport Accident Investigation Commission as it looks into what happened on NZ99 so couldn't comment at this stage.