The Government is accused of "steamrolling" transport solutions on Wellington for the sake of a Labour-Greens relationship.
Several city councillors have told the Herald they felt they were presented with a "take it or leave it" deal over Let's Get Wellington Moving ahead of a council vote to support the package.
They claim mayor Justin Lester told them Associate Transport Minister Julie Anne Genter threatened to resign over the project during negotiations.
Wellington City councillor Diane Calvert said she was left with the impression the confidence and supply agreement with Labour could have been in jeopardy if the Greens hadn't got their way.
Lester has denied the claims. Meanwhile, Genter has said the agreement was never put in jeopardy and she never threatened to resign.
Wellington based National list MP Nicola Willis said the situation called into question the legitimacy of the $6.4 billion transport package.
"What it suggests is that councillors were not able to act in the best interests of Wellingtonians but were instead politically strong-armed into accepting a deal they didn't like," she said.
The revelations have come in the same week the Chief Ombudsman launched an investigation into the secret letter Genter penned to Transport Minister Phil Twyford about the project in March.
Genter is refusing to release the letter fuelling speculation around the political influence the Greens had over delaying a second Mt Victoria tunnel.
Meanwhile, a second Terrace tunnel and the trenching of Karo Drive didn't make the final cut at all.
Calvert said Lester portrayed the Government-endorsed package as the best deal they were going to get, leading her to question whether local government pushed hard enough at the negotiating table.
"There seems to be some heavy political, ideological, influence happening, and as an independent not aligned to any particular party I have real concerns about what's happened."
Councillor Andy Foster said the Government was essentially imposing its solutions on the city.
"Local government, in consultation with its communities, should try and shape their cities, these are things that last for a very long time and transport is a key part of that.
"Central government shouldn't be steamrolling over the top and be designing the city for you."
But Genter said the package would deliver what Wellingtonians said they wanted during consultation, which was a world class public transport system and safe walking and cycling.
Wellington City councillors unanimously voted to support the LGWM package in June.
"For me, we voted yes because if we voted no, we would have ended up with nothing", Foster said.
"At the very least after three years of nothing happening we need to get on with the so called quick wins… but I think some of the bigger things are going to need a lot more thought and I don't know that there's a great deal of conviction that they are the right things for us to be doing," he said.
Lester said it was disappointing to see some councillors "scrambling" for publicity ahead of local body elections.
"I'm not interested in gossip or indulging people's speculation."
Lester said he had been involved first-hand with the negotiations and could confidently say local government put its best foot forward.