Aucklanders have been told that if they want tunnels for their new harbour crossing instead of a new bridge, they might have to dig into their own pockets for the $1.4 billion difference.

A Transport Agency report issued yesterday estimated the cost of a bridge at up to $3.9 billion, whereas two three-lane tunnels would cost $5.3 billion.

A new crossing is needed within about 20 years to cope with the city's growth and to bolster the ageing harbour bridge.

A new bridge would run close to the existing 52-year-old structure, diverging from it at Northcote Pt and then forming a triangle to the Auckland isthmus through Westhaven.

Auckland Council transport chairman Mike Lee said the combination of new and old bridges would make the city look "pug ugly" and would not increase transport resilience, given how close together they would be.

He said the Transport Agency had revived the bridge option, which was ruled out in a 2008 study, at the behest of Transport Minister Steven Joyce.

He accused the minister of a highly political interference in Super City planning aimed at undermining the $2 billion central rail tunnel loop project.

But Mr Joyce and the Transport Agency both say they have not yet formed a view on whether the next crossing should be a bridge or tunnels.

The agency indicated, however, that Aucklanders might have to dig into their own pockets if they wanted tunnels.

"Where Auckland has a different set of preferences from the national focus on benefits and cost, it may be appropriate that these preferences are partly funded by a regional contribution," it says in a covering document.

Mr Joyce indicated some concern at the substantial extra cost from that estimated in the 2008 study of $3.7 billion to $4.1 billion for a set of four harbour tunnels, two for motorway traffic and two for trains.

He acknowledged that benefit-cost ratios were "not great" for either a bridge or a tunnel.

The latest report - the sixth on a new crossing since 1986 - estimates that the return from motorway tunnels in terms of transport benefits but not wider economic impacts would be a meagre 40c for each dollar invested.

A bridge would be little better in providing just 60c, the difference largely being because it would take less time to build - about five years compared with seven for tunnels.

But Mr Joyce said there would be a strategic need for another harbour link within 20 years, before the clip-on lanes of the old bridge would need replacing, although he understood a newly completed $86 million strengthening project had "moderated" the Transport Agency's view about their longevity.

"It's still within a 20-year cycle but I think they've got a bit less urgent about when."

Both a bridge and tunnels would cater for public transport, cycling and walking lanes - but not trains.

The agency estimates that a rail tunnel, which the new report indicates would be difficult to justify for 30 years, could add $1.6 billion to the bill.

It has ruled out knocking down the existing bridge - which promoters of an Anzac centenary crossing want - saying it needs the resilience of two transport links across the harbour.

Mayor Len Brown said it was appropriate that the report stopped short of recommending a preferred crossing, given Prime Minister John Key's support for the Auckland spatial plan process starting this morning.

He said that although the report indicated a marginally higher investment return from a bridge, it predicted that obtaining consent for such a structure instead of tunnels would be "improbable" in the existing statutory and policy environment.

"My initial view is that the tunnel option makes more sense," Mayor Brown said. "However, I want to hear Aucklanders' perspective on the options available. Tunnelling technologies are advancing quickly and many countries are building combined road and rail tunnels that would future-proof our system."

Although the report says the Northern Busway and an extension to Orewa will serve northern Auckland's public transport needs for another 30 years, Mr Brown said a cross-harbour rail link was needed to make the region's overall network run properly.

"Getting our transport system right is not negotiable if the new Auckland is to achieve its potential as ... the economic powerhouse of the nation."