The ferry's next scheduled sailing is for 8pm on Sunday.
This is the second time the Stena Alegra has run into trouble since it began services in January.
Less than a week after it made its first Cook Strait crossing, it broke down after suffering a partial loss of power while leaving Wellington.
At the time, one freight-only sailing and one passenger sailing across Cook Strait were cancelled.
Meanwhile, the company's Aratere ferry, which was sidelined after losing its propeller during a Cook Strait crossing in November, is undergoing further repairs, after rudder cracks were discovered.
The ship, which is in dry dock in Singapore, has had several repairs, including the reinstallation of new shafts, old propellers and stabilisers, in preparation for sea trials.
"When reinstalling the rudders this week, ongoing checks identified a crack in the ship's port and starboard 'rudder stock' - that is, the shafts which turn the rudders,'' KiwiRail said.
The KiwiRail spokeswoman said Interislander's other ferries were still sailing.
Passengers and freight companies were being contacted by the company so alternative arrangements could be made, she said.