Interislander says it has cancelled Kaitaki sailings up until Wednesday afternoon as a safety precaution after the starboard bow door was impacted by a large wave while crossing from Picton to Wellington on Monday afternoon.
Interislander General Manager Operations Duncan Roy said a surveyor was on-site this afternoon and repairs were under way.
"The ferry Aratere is running an additional return sailing today and Thursday to help accommodate disrupted customers who we are contacting directly. These additional sailings are freight-only."
KiwiRail said the damage did not affect the safety of the Cook Strait ferry.
"During pre-departure preparation on Monday night the door could not re-align before closing," Roy said.
"For safety reasons we have cancelled sailings while the damage is assessed in more detail and repairs are completed, under the guidance of our third party class authority."
The Kaitaki ferry has faced a number of mechanical issues already this year.
Earlier this month an issue with the steering forced passengers to spend the night on board the ferry.
The ferry has also been subject to an investigation by the Transport Accident Investigation Commission after it lost power in January.
All of Tuesday's sailings on the Kaitaki were cancelled, as well as a 2.30am sailing from Picton on Wednesday.
To compensate, sailings on the Aratere have also been moved forward and an additional 10.45pm from Wellington and 2.45am return from Picton will be added. This sailing is freight only.
MetService currently has a gale warning in place for the Cook Strait.
Interislander said it was monitoring the situation closely.
Bluebridge said sailings were going ahead, but "they will be rough and may take longer, resulting in delays".
MetService said the rough seas were expected to ease later today.