The Horizons Regional Council will continue with its nutrient management consenting ahead of a date with the Environment Court.
Last week, Fish & Game and the Environmental Defence Society filed declaration proceedings against the council.
The groups are concerned about the council's management and implementation of the One Plan and its consenting of intensive agriculture under it.
In a report to councillors by Horizons regulatory manager Nic Peet said the court proceedings could cost more than $500,000, including operating costs and staff time.
Dr Peet's report said depending on the outcome there was a low but potential risk council would need to revisit consents already issued.
On Thursday, the council voted to continue the consenting process but for it to be under regular review by chief executive Michael McCartney.
The council will seek legal advice on whether it should join the declaration proceedings and if it could enforce failure to submit consent applications.
An invitation will be sent to Fish & Game and EDS to meet with council.