The New Zealand Transport Agency is rejecting claims a second Auckland harbour crossing will not include rail.
The Green Party said the agency was safe-guarding a road-only crossing between the central city and Northcote Point, and that a rail option might be shelved.
The party launched a campaign to build a rail crossing to the North Shore by 2030, and said the government had prioritised a road-only option.
It said a rail-only tunnel bridging the city and Northcote Point would reduce congestion and be $2 billion cheaper than the $4-6bn price tag currently proposed by the NZ Transport Agency (NZTA).
Transport spokeswoman Julie Anne Genter said NZTA was ignoring this option altogether, and cited a memo released in June suggesting a decision on what the final crossing would look like would be left up to Auckland Transport.
"NZTA at the moment is spending $27 million to designate a road-only option, and this reflects the lack of integration in transport planning and funding that we've long called on the National government to change.
"It would make more sense to take a more integrated approach to planning and funding, and the NZ Transport Agency is the logical body to be leading that."
The NZTA memo was released under the Official Information Act to Auckland researcher Matt Lowrie who edits the Transport Blog.
He said the Greens might be jumping the gun, and said the memo related to the land designation process.
"The information shows that the NZTA themselves weren't looking at it, but they were leaving it up to Auckland Transport.
"Part of our role in highlighting it is to make sure it doesn't get forgotten."
NZTA said any suggestions that it was focusing on a road only solution were "misleading and inaccurate".
In a statement, its Auckland regional director Ernst Zöllner said the agency was "100 percent committed to providing Aucklanders with a future multi-modal transport corridor that would work in conjunction with the Auckland Harbour Bridge".
He said the details of the project had not been finalised yet and the agency was working with Auckland Transport to investigate which type of rapid transit would be best.
"This information will feed into the Additional Waitematā Harbour Crossing project and ensure the protected route enables and is fully integrated with a future public transport network."
But Mr Lowrie was worried that if a decision on rail was not made now, it could be more difficult later on.
"You also need to know how it connects on either side, because if you don't sort that out right now something could be built that prevents it from being used.
"While the crossing could include rail, the connections on either side might preclude it."
The office of the mayor Len Brown also issued a statement, saying Mr Brown was committed to getting rail to the North Shore, and any proposal for a second crossing should include it.