The interislander ferry Aratere is out of action until Thursday afternoon.
A KiwiRail spokesperson says the ferry, one of three it owns, has a problem with its propulsion system.
A 10.30am sailing from Picton to Wellington and a 2.30 return trip on Wednesday were cancelled, along with a 6.30pm sailing from Picton to Wellington.
Passengers were put on other services.
Two freight services were also cancelled and freight has been transferred to other services.
KiwiRail says the ferry should be back in service by 2.30pm on Thursday.