The interisland ferry Aratere is still under warranty from its Singaporean refit.
KiwiRail chief executive Jim Quinn says the cause of its repeated engine failures remains unclear, but if they are a consequence of the refit the contractor may have financial liability.
Mr Quinn has rejected a claim by New Zealand Shipping Federation former head Rod Grout that lengthening a ship could be destabilising.
The ferry has had a series of mechanical problems since a $53 million refit in April, when the Aratere was lengthened by 30 metres.
Maritime New Zealand has stopped the ferry from sailing until KiwiRail can prove it is safe.
Mr Quinn says ships can be stretched safely and he is optimistic the problems are just a tuning issue. He says the Aratere will operate well.
Mr Quinn says that while six sailings on Thursday are cancelled, he is hopeful the Aratere will be back in operation on Friday.
About 500 passengers and further freight customers have been affected so far on Thursday.
Used to it - Mainfreight
Mainfreight Wellington transport manager Paul Fincham says that while there has been minor inconvenience from the cancelled Aratere sailings, delays have lasted a matter of hours rather than days.
He says communication has been good and they are used to working without the Aratere, which was out of action for five months while it was refitted.