The Prime Minister yesterday poured cold water on Super City Mayor-elect Len Brown's ambitious plans for rail, indicating the Government was closing its chequebook for extra projects.

John Key, who with Transport Minister Steven Joyce is prepared to spend an extra $1.6 billion on what has been dubbed the "holiday highway" from Puhoi to Wellsford, said ratepayers would have to pay for Mr Brown's plans to fast-track rail.

The PM said the Government shared the goal of an efficient transport system for Auckland, but "not all roads, or all rail tracks, can lead to the Government".

"There is no free lunch when it comes to any of this stuff," he said.

"The Government is spending $5 billion in Auckland. We're spending $1.6 billion on rail and that's a considerable contribution already."

The rail money is for double tracking, electrification and new rolling stock for suburban rail.

But Mr Brown also wants a central-city rail loop, a link to the airport and a line over a new harbour crossing to the North Shore, all over five to 15 years.

Said Mr Key: "Ratepayers will also have to pay their fair share. I don't think Auckland can expect central Government to pay all of the costs. It's just not realistic because if we did that in Auckland, why wouldn't we do it around the rest of the country?"

Asked if he was concerned about the Auckland Council taking on debt to pay for rail projects, the Prime Minister said it was up to each council to decide on its debt levels.

"There are guidelines on how much debt they can realistically have and service. If they issue too much debt, rates have to go up to pay for that."

Mr Key and Mr Joyce hope to meet Mr Brown before Friday to discuss his ambitions as the first mayor of the Super City, which covers 1.4 million Aucklanders and has an annual budget of $3.2 billion.

Last night, Mr Brown played down the Prime Minister's comments, saying discussions on paying for rail projects would take place over years, not three days after an election.

"I'm aware that the Government sees itself in a situation of challenging financial times," he said. "It is coming through the back end of a recession."

Mr Brown said his rail plans were set in the short, medium and long term and had four possible cash sources.

These were city and Government funding, infrastructure bonds and private-public partnerships.

He said the Government wanted Auckland to turn itself into "much more of an economic powerhouse" than it was now, and transport and fixing congestion were important parts of that.

Asked if the Government should be placing the Puhoi-to-Wellsford motorway project ahead of rail, Mr Brown said that was a discussion that needed to be held.

Even without the attraction of double-tracking and fast electric trains, rail patronage in Auckland has soared since the construction of the Britomart transport terminal in 2003 - from 2.5 million to 8.5 million passengers a year.

Mr Key said yesterday that he did not expect to appoint a minister to deal specifically with the Super City, saying such a concept had failed when Labour tried it with Judith Tizard.

But he expected ministers in relevant portfolios to stay in close touch with the Auckland Council.