Court action over the One Plan will discourage intensive farming operators from applying for the required resource consents, say Horizons Regional Council.

On Wednesday Fish & Game and the Environmental Defence Society announced they would be lodging declaration proceedings in the Environment Court this week.

The groups are concerned about the council's management and implementation of the One Plan and its consenting of intensive agriculture under it.

The pending court action was discussed briefly at the council's Environment Committee meeting on Wednesday.

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Regulatory group manager Nic Peet said it would put pressure on staff time and impact on consenting in the region.

"Those proceedings... draw on resources through the regulatory team to service those kind of court proceedings," he said.

Committee chair Colleen Sheldon asked if the court action would put a halt to the One Plan consenting process.

Horizons chief executive Michael McCartney said he understood some farmers had indicated they no longer wanted to pursue their applications.

"In essence it creates a level of uncertainty and that uncertainty affects consent applicants," he said.

"This is the consequence of these proceedings and we need to have a position on that, frankly.

"Do we force these people to go through that consent process or not?"

Mr McCartney said the matter would need to be considered at next week's council meeting.

Meanwhile, Dr Peet said it may be harder to force intensive farming operations into consents while the regime is before the court.

"Obviously the plan remains operative for people who are consented. I think there's a fairly good case we can continue to work on the compliance with their consents," he said.

"I think council will find itself in a much weaker position if somebody has declined getting a consent, or is refusing to get a consent," Dr Peet said.

"While this process is going on our ability to enforce in that situation is probably going to be significantly compromised."

Horizons chairman Bruce Gordon said the court action was disappointing because Horizons had made progress in terms of water quality.

"We have always had an open door policy for anyone who may have concerns. It's unfortunate that EDS and Fish & Game have not chosen to utilise this process.

"It's not a box ticking exercise, it's about proper nutrient management to ensure the best possible outcomes for both our rural community and our region's water quality.

"While the court proceedings are a distraction we hope that it will add valuable data to our ongoing review of the plan rather than an unnecessary cost of up to half a million dollars at the expense of our ratepayers."

Horizons natural resources and partnership manager Dr Jon Roygard said "significant reductions" in nitrogen leaching had been made.

"The existing dairy farms consented have made significant reductions in the leaching of nitrogen at an average of nine per cent."