The megaferries, three times the size of existing interislanders, are due to arrive in the next four to five years.
But there's disagreement about where to moor them, and nothing is yet designed.
KiwiRail wants them at Kings Wharf, nearer to central Wellington.
But council and other harbour users say the big new Interislanders should share a site at Kaiwharawhara with its rival Bluebridge.
Greater Wellington Regional Council chairperson Daron Ponter said a multi-use ferry terminal was more efficient, particularly in terms of things like carparking.
"If you're taking your car as you go into the facility, you're not making a choice between whether you go to Bluebridge or whether you go to the Interislander, you're going to the next allocated carpark, for the next ferry and there's no distinction made.
"So, the facilities right from the carparking, to the counter facilities in the terminal are being shared, just as they are in an airport," he said.
Ponter says to meet KiwiRail's timeframes and have the wharf ready for 2024 they would have had to start the design two years ago.
"The ferries can't go anywhere else, it's not as if they can park up at any of the existing facilities that we have. The existing facilities at Centreport just cannot cater for these ferries, so if we don't get it right and the timings not right, they just won't be berthing," he said.
Ponter said because it can't reach agreement with KiwiRail, they're left with no option but to have an interim facility, which means Bluebridge would stay at its current site on Kings Wharf until 2026.
"Doing the transition approach is likely to be more expensive than if we'd had more time and were able to put in a multi-uer facility. If KiwiRail is committed to having these ferries by 2024 or 2025 then that's no longer going to be possible, we are going to have to go to a transitory approach," he said.
Ponter says the full costs of the project aren't known because the detailed design hasn't been done.
Information released by the Treasury, puts KiwiRail's costs at $925 million, that includes designing and building the new ships, its contribution to the ferry terminal infrastructure and paying for consultants and experts.
It doesn't include the likely huge cost of rerouting roads and other infrastructure.
Wellington City Councillor Nicola Young said, given the sums of money involved, it might be a good time to pause for a cup of tea.
"KiwiRail should slow down their ferry renewal programme, push the deadline out. This is a huge investment and it's critical for our county's transport, freight and quality of life to have the State Highway One going across Cook Strait. We've got to make the right decisions and the right decisions take time," she said.
Ponter agrees, questioning whether it's the right time to be making bold decisions on very large ferries.
"Should we be looking for some transitory arrangement where KiwiRail purchases second hand ferries for a period and we move to a new model, over a longer period of time," he said.
Joe Fleetwood, general secretary of the Martime Union, said his organisation supported the decision to buy bespoke ferries, which had worked well in the past.
"The old Aramoana, Arahanga, Aratika and Aranui, so if you purpose build them and pay outright, kept for their duration - maybe 15-20 years - they'll have probably paid for themselves, maybe 10-fold," he said.
In a statement KiwiRail says it's still in discussions with the regional council and CentrePort about the location of the new terminal and denies that Kings Wharf is no longer an option.
This despite a study by CentrePort, which has found Kaiwharawhara was the preferred site for the new terminal. This was consistent with the findings of an earlier report released in April.
Ponter says the council will apply to the government for fast-track legisation to speed up the design and building process.
Meanwhile, city councillor Nicola Young has filed a notice of motion that the council support the building of a new multi-use ferry terminal at Kaiwharawhara.
It requests Mayor Andy Foster communicate this to KiwiRail's shareholding ministers Grant Robertson and David Clark.
The notice, which states the council's opposition to KiwiRail's plans for a new terminal at Kings Wharf, was signed by all 15 councillors yesterday. Councillors will vote on it at a council meeting on 16 December.