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The ferry had resumed passenger sailings just two days ago, five weeks after it lost power and issued a mayday call in Cook Strait.
The latest engineering issue with vessel was discovered yesterday evening.
A passenger sailing on the Kaitaki was due to depart from Wellington at 8.45am today.
Interislander executive general manager Walter Rushbrook said affected passengers were notified last night by email and text message.
“We expect to move all passengers and vehicles booked on scheduled Kaitaki sailings today on to Kaiarahi and Aratere sailings,” said Rushbrook.
“We are also planning additional Kaiarahi and Aratere sailings on Monday to move passengers, vehicles and freight.”
Rushbrook said the issue was unrelated to the vessel losing power on January 28 and that they were working hard to resolve it quickly.
“We appreciate the inconvenience this causes passengers and our customers, particularly given Kaitaki only resumed carrying passengers on Saturday,” he said.
Rushbrook said an update on the Kaitaki would be made in 24 hours.
The engineering issue comes as both Interislander and rival operator Bluebridge have been hit with breakdowns and engine problems in recent weeks, disrupting the travel plans of thousands of passengers.
At the end of January, all four engines on the Kaitaki shut down and the ship drifted a nautical mile (1.8km) towards Wellington’s south coast before the ship’s anchors held and power was able to be restored.
On Friday, Interislander announced that the Kaitaki would resume passenger sailings.
At the time, Rushbrook said since the vessel’s mayday incident, several assurance processes had been undertaken to confirm ferries in the fleet were safe to sail.
“We have also had a number of independent checks undertaken. The maritime industry is highly regulated, so it is not our decision alone to sail the ships,” Rushbrook said.
“We have had the all-clear from surveyors from our Class Authority, our team has been through all our ferries checking parts and systems, and we have worked closely with the regulatory authority, Maritime New Zealand.”
The return of passenger sailings on Kaitaki was hoped to help ease pressure on the troubled Cook Strait services.