Officials have signalled Let's Get Wellington Moving (LGWM) is headed towards a budget blowout as they try to get the $6.4 billion transport project back on track.
Transport Minister Michael Wood confirmed he has seen initial indications of bigger projects potentially costing more than first thought.
But he says Wellingtonians will see spades in the ground on smaller projects by the end of the year.
LGWM is a three-way partnership between Wellington City Council, Greater Wellington Regional Council, and Waka Kotahi NZTA.
Big projects in the plan include mass rapid transit from the city to the airport and doubling the Mt Victoria Tunnel.
On Tuesday night funding partners met with Wood after a review of the project found leadership problems, a detrimental culture, inadequate resourcing, and ultimately that it was at risk of failing.
The programme's governance structure and leadership team is getting a major shake-up as a result.
Work is also under way to address longer-term affordability issues and ensure the project has the funding it needs.
Officials have signalled "likely increases in costs compared to the earlier indicative package".
The LGWM Partnership Board issued a statement this afternoon following their meeting with the Minister.
Their new plan includes appointing an independent chairperson to the board.
Some of programme director Andrew Body's responsibilities will also be divided up.
A deputy programme director, with expertise in helping teams work collaboratively in joint ventures, will become part of the programme's leadership team.
An additional programme director will also be appointed to oversee a new short-term three-year programme to finally secure what were meant to be "quick wins".
These include walking and cycling improvements as well as bus priority measures.
Specifically, this programme encompasses the Golden Mile, Thorndon Quay & Hutt Rd, the Cobham Dr crossing, and walking improvements in the central city.
Wood told the Herald there has been a "real wake up call" for the LGWM programme.
He expected spades to be in the ground on walking improvements in the central city and at Cobham Dr by the end of the year.
"Our job is to put our noses down and move forward with the delivery... we need to develop a sense of momentum and give people some confidence in the programme."
But Wellington-based National list MP Nicola Willis said people expected progress on key infrastructure projects.
"I'm like most Wellingtonians, I have lost patience with the delays and the excuses.
"What we want to see is the Basin Reserve sorted out, the tunnel sorted out, and modern public transport. What we're getting is new job titles and discussions about new footpaths. It's not good enough."
She said the Government needed to provide leadership and be clear about what projects it would be funding and in what order.
Every year of delay would cost the city more, Willis said.
"This is a result of an unclear mandate from the Government, a lack of clarity between the key partners, and therefore the ongoing soup that is the Let's Get Wellington Moving programme."
Wood argued that realistically, projects of such scale took time to develop and get right.
"Wellingtonians would expect us, when we're dealing with billions of dollars of public money, to make sure that we have sound and well worked through business cases before us, that we do work within the significant fiscal envelope that we've set up for this programme. The money is not limitless."
He confirmed there were initial indications of potential cost increases on bigger projects, but would not elaborate further saying he did not have "full information" yet.
"That potentially means that we need to think really carefully about what we prioritise, it means we look at things like the phasing of projects, but whichever way we cut it, this will be the biggest investment in Wellington's transport infrastructure in generations.
"I'm confident that we've now got the parties around the table to make some good decisions about that."