Official papers from the Ministry of Transport reveal it has concerns about the Government's involvement in developing rail in Auckland.
A briefing to Transport Minister Stephen Joyce also shows the ministry's opposition to a regional fuel tax to help pay for rail.
The regional fuel tax - designed to help pay for Auckland's transport plans - was due to have come into effect on 1 July, but was abandoned by the Government in March.
As well, the Government has put the ministry firmly back in control of all transport planning, pushing the Treasury to the sidelines.
Papers obtained by Radio New Zealand under the Official Information Act reveal the ministry was opposed to a regional fuel tax even though the Treasury did not share its concerns.
Transport Minister Steven Joyce says it was clear to him the Ministry of Transport had deep concerns about the regional fuel tax planned for Auckland and other regions around the country.
In papers to Mr Joyce, the ministry also expressed deep concerns about the plans for developing the rail network in Auckland, saying it remained an ongoing technical and fiscal risk to the Government.
It made the point that it had not been involved in advising on recent rail investments under the previous Labour Government.
Mr Joyce says changes have been made to ensure the ministry is the lead department in transport, including rail.
Labour Party transport spokesperson Darren Hughes says the spat between departments has undermined Auckland's plans to upgrade its transport system, particularly the train network.
