The second phase of works would involve adjusting the fenders to go back into place so that the Manannan can operate across the summer and then Manxman can go in there next winter, Haywood said.
The Steam Packet said sailings to and from Liverpool on 1 and 2 November will now operate to Heysham, with coach transfers to Liverpool Terminal provided for affected passengers.
Managing director Brian Thomson said: “We know this is frustrating and disappointing for passengers.”
But by limiting the changes to these two days, he said he hoped “the necessary works can be undertaken” to offer consistent weekend sailings to Liverpool for the rest of the winter.
The final cost of the project has not yet been confirmed but the last estimate was about £70.6m.
Haywood said the issue with the fender stemmed from “something that’s gone wrong in the very early stages of this project”.
She said: “Everything has been installed in line with the original design but the original design didn’t actually match what we were hoping for.”
The DOI was therefore “in the middle of extensive legal negotiations with designers and other companies that were involved in the project”, Haywood said.
Meanwhile the department has employed contractors in Merseyside to carry out the repairs and said it was working with the Steam Packet to “minimise disruption”.