Treasury warned Phil Twyford against committing to the proposed Wellington transit package because it was "based on several assumptions".
A Cabinet paper announcing the Let's Get Wellington Moving (LGWM) package - which the Government endorsed on Thursday - noted several concerns by Treasury.
"Treasury does not support the Minister of Transport's recommendation that Cabinet endorse the indicative LGWM package," the paper reads.
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"Making an announcement at this stage carries significant risks, as it will raise public expectations of future investment before the costs and benefits of the package are fully understood."
The paper goes on to question the proposal in that it "relies on several assumptions that have not been thoroughly tested, including exploring long-term financing to fund rapid transit".
Twyford defended the announcement, telling Newshub: "Cabinet decided to endorse the indicative package because Wellingtonians have waited decades for transport investment that will unleash our capital city's potential."
He said the package will ease congestion in the city of over 400,000 people, and will also make it safer and easier to get around, and boost growth.
"Officials have done a lot of work crunching the numbers and looking through the cost implications, including on long-term financing for rapid transit.
"I will report back to Cabinet with a long-term financing proposal in due course."
National's transport spokesperson Paul Goldsmith told Newshub his party supports getting Wellington moving and wants to see the LGWM projects developed.
But he said the proposal is nebulous in that it "talks about things happening over the next 20 or 30 years - very vague ideas about how it's going to be paid for by the Government and by the local community".
"What we need to see though is very clear, rational arguments about the costs and benefits of it so that we can make rational decisions - not just racing out making announcements without doing the homework."
When asked why the Transport Minister would ignore the warnings, Goldsmith said: "He's a minister under serious pressure and he knows that he hasn't delivered in housing, and so he's desperate for an announcement."
What is Let's Get Wellington Moving?
Four future transport scenarios for Wellington that composed of various transport improvements and infrastructure were put out for public consultation in late-2017.
Public input was used to develop a recommended programme of investment. Since then, the LGWM package components have been evaluated and an indicative package and funding arrangement has been endorsed by Cabinet.
The LGWM package has proposed an extra Mt Victoria tunnel, integrating modern rapid transit, walking and cycling upgrades, and providing better public transport alongside the city's motorways and roads.
To be delivered over about 20 years, the $6.4 billion package includes larger scale projects which Twyford said will involve more detailed business cases, and planning approvals will be delivered later on.
The cost will be split 60:40 between ratepayers and the Government. The latter will contribute $3.8 billion over 30 years from the National Land Transport Fund into which all fuel excise duty, road user charges and motor vehicle relicensing fees are paid.
However, the Wellington City Council and Greater Wellington Regional Council still need to confirm their commitment to funding their share of the project.