There was no fire but the ship's engines were shut down while an alternative fuel supply was switched on.
The Aratere then continued its crossing at up to 13 knots and was met by a tug at the heads of Wellington Harbour as a precautionary measure.
The ship berthed without assistance at 11.40pm, about two hours later than scheduled.
Interislander general manager Thomas Davis said the crew and 142 passengers aboard the KiwiRail-owned Cook Strait ferry were never in any danger and were kept informed throughout the sailing.
Mr Davis said the captain made several announcements during the voyage to reassure passengers.
Eight sailings of the Aratere today and tomorrow have been cancelled while the problems are investigated.
The incident comes after the Aratere had a problem with its port shaft and needed assistance from tugs due to bad weather on October 6.
The Aratere returned to service in September after a five-month, $52 million refurbishment in Singapore that added a new bow and 30m to its mid-section, boosting its capacity.
Mr Davis said the problems were not directly linked to the ship's recent extension.
He apologised to passengers and freight customers who were disrupted but said safety was paramount.
"The causes of the incident will be identified and fixed before the ship sails again. We apologise to our customers, and are contacting them to move to other sailings.
"We are disappointed to have these disruptions in our service to our customers, and we are working hard to rectify them."
Interislander ships were professionally crewed and KiwiRail would co-operate with any investigations.
