A KiwiRail spokesperson said the Kaitaki left Wellington at 8.45am and experienced significant rolling about 10.30am when it passed near the Karori Lighthouse.
The spokesperson said some passenger vehicles shifted and sustained minor damage. One passenger sustained a minor injury and was given medical assistance by the crew.
Interislander is supporting affected customers and a full assessment is being carried out.
Two other Interislander ferry crossings - the 6.15am from Picton and the 11am return service - were cancelled as strong winds pummelled central areas of the country.
Meanwhile, Interislander has provided passengers with tips to avoid seasickness for other sailings.
It said anyone who was worried about seasickness should sit at the back of the ship and should not sail on an empty stomach.
Bluebridge said the stormy weather had forced the ferry operator to cancel its two Picton-bound services, and three Wellington-bound services for Friday.
It had put on four additional sailings for this weekend, and rescheduled some services, to accommodate those who could not travel today.
A lingering low-pressure system is bringing rain or showers to many parts of New Zealand, with thunderstorms, large swells and strong winds affecting the centre of the country.
