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The overspend amount is about twice as much of what council staff had anticipated during lengthy plan change 13 talks which concluded last month.
The expenses are to be funded from the board's general reserves which was passed by members at last week's board meeting in Cromwell.
Costs in providing evidence to support the council's submission during the recent plan change hearing included legal and professional fees.
A submission was made by the council when asked to by the community board.
A report by council planning and environment executive manager Louise van der Voort said the council made the decision to lodge the submission recognising the scale of plan change 13 and the effect it could have on the outcomes of the Cromwell Masterplan, and the future of Cromwell and its community.
"Whilst unbudgeted, it was considered appropriate to support the investment of the masterplan by presenting legal submissions and expert evidence at the hearing."
A hearing on a plan by the Winton Group for a 900-lot residential development on the outskirts of Cromwell was first held on June 10-14.
The hearing reconvened on July 2-5.
The plan has been met with opposition by residents and community leaders.
During a presentation at Tuesday's board meeting, Ms van der Voort said she was surprised by the costs.
"I thought it would be about half the amount.
"We had never had a private plan change hearing go on for that length of time."
Board chairman Neil Gillespie said he was not surprised by the amount of the bill.
Board member Robin Dicey queried why the board had to fund extensive costs for a council submission.
He also expressed fears costs could blow out should the Winton Group take legal action.
Ms van der Voort explained to the board there was a possible conflict of interest, had the council funded a submission.
"We [the council] can commission reports but this evidence is different."
The level of work preparing evidence and extensive public consultation during the master plan process would hopefully be given weight by the commission, Ms van der Voort said.
She said it was a unique situation for the council to be in, sentiments echoed by Mr Gillespie.
Speaking to the Otago Daily Times, Mr Gillespie said the board went into the submission process knowing there would be costs to be paid.
"By getting council to prepare the submission, the board wanted to protect that investment made in the masterplan," he said.
"You can run the argument either way as to who pays.
"It's all council money. You could argue that council should have been paying for the whole masterplan process as well."
No date has been set for a decision around plan change 13.