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The concern was raised as Dunedin city councillors discussed a proposed change to NZTA's financial assistance rate (FAR) at the Dunedin City Council infrastructure services committee meeting yesterday.
The FAR was used to determine how much money was allocated from the national land transport fund to help pay for roading projects around the country.
The NZTA was consulting councils as part of a review of proposed changes to the FAR, and planned to introduce any changes next year, ready for the 2015-18 national funding round.
The details were contained in a report by council transportation operations programme engineer Michael Harrison to yesterday's meeting, which warned the changes could have implications for council budgets.
The NZTA review included considering whether FARs should be used to encourage particular activities or approaches, such as ''land transport activities aimed at unlocking the future potential of an area''.
That worried Cr Richard Thomson, who wondered if the wording was ''code for redirecting large quantities of it at Auckland transport issues''.
Asked by Cr Thomson what the wording meant, Mr Harrison said council staff ''don't have any idea'' and NZTA was not yet prepared to say.
That prompted Cr Lee Vandervis to conclude: ''It would suggest that your suspicions have some weight, I would have thought.''
Council operations general manager Tony Avery said it was already known funding for new roading work was constrained, and there was not enough money to go around.
As a result of the review, it was possible funding adjustments could come at the expense of ''some rural centres or places south''.
Mayor Dave Cull said, alternatively, it was possible the economic benefits of maintaining rural roads - used by dairy tankers, logging and sheep trucks - could be underscored when compared with Auckland's motorways.
The council planned to prepare a submission on the review, outlining its concerns, to be prepared by council staff with help from Mr Cull and Crs Andrew Noone, Syd Brown and Kate Wilson.