The Interisland line says all passenger sailings on the Arahura are cancelled for Thursday and Friday.
The ship will still make freight sailings because fewer crew are needed.
However, one ferry will not be carrying passengers until at least Saturday.
General manager Thomas Davis says this problem has arisen following the suspension of a sailor after a near-miss in Cook Strait off Karori lighthouse on Monday.
He says this led to two cancellations on Wednesday and more on Thursday and Friday because relief personnel are unavailable.
Mr Davis says set number of crew have to be available for a sailing with passengers for safety reasons, and this has not been possible to achieve.
Relief crew have been used to cover recent sickness and bereavement and are unavailable to fill in for the suspended seaman.