Trout habitats are protected under the Resource Management Act, but they also eat native fish (File photo).

A move by a council to get clarification from Conservation Minister Eugenie Sage on balancing the interests of trout and native fish protection has been labelled by Fish and Game a "direct attack" on its interests.

But Sage says some of Fish and Game's lobbying to protect trout habitats has also helped native fish.

Horizons Regional Council is in the process of drafting a letter to the conservation and environment ministers, asking for their views about trout and salmon protection.

In a draft letter presented to the council's strategy and policy committee on Wednesday, the reasons for the query included trout being among the most significant invasive species that affected native ecosystems.

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The letter said freshwater management and improvement was affected by having to protect trout in areas important for native aquatic biodiversity.

Furthermore, it raised conflicts in the Resource Management Act. Section 6 of the act places the protection of indigenous fauna as a matter of national significance, but the next section requires "particular regard" to protection of trout and salmon habitats

Councillor Wiremu Te Awe Awe said iwi would wholeheartedly support the council sending the letter.

Cr John Barrow was also supportive.

"If anyone is speaking on behalf of iwi here, it's Wiremu, and it is a powerful voice to support."

Cr Lindsay Burnell said it was not about being anti-trout, but trying to ensure the protection of native fish.

"I believe the native species have been led to the slaughter for too long."

Cr Gordon McKellar wondered if the best solution was to remove the need to have a game fishing licence to catch trout.

"I think it's good to start the conversation and see where we get to."

Fish and Game Wellington council regional manager Phil Teal described Horizons' move as a "direct attack" on its interests, and a response to a 2017 Environment Court judgment that found Horizons was not correctly implementing the One Plan.

The One Plan is the document the council uses to dictate how natural resources are managed in Manawatū-Whanganui.

The judgment found Horizons was not doing enough to keep streams and rivers clean, and incorrectly issuing consents for dairy farming.

"Horizons need to focus on the real problems of intensive agriculture and habitat loss affecting our waterways, and deal with these issues now, if they are truly interested in freshwater improvement and ecosystem restoration," Teal said.

Trout and salmon had the highest requirement for water quality under the Resource Management Act, which had the side-effect of creating more areas of clean water in rivers and lakes for everyone, he said.

"Native species have a far higher threshold for water pollution than trout, which means more headroom for intensified farming and all the negative impacts on water quality that come with it."

Sage said she was aware of the issues native fish species have, with more than 70 per cent of them threatened with extinction due to such things as drainage schemes and habitat loss.

Trout and salmon did eat native fish, but there were also many people who liked angling, she said. While the Department of Conservation had not made its voice heard strongly in the past few years about waterway protection, supporters of trout had helped native fish populations.

She cited Fish and Game's work to improve river flows for trout and salmon fishing, noting those conditions also helped native fish.

"It is the flow rates that have been the biggest battle ground with increasing irrigation and extraction of water."

The department had been asked to better implement its responsibilities under the Conservation Act to get involved when applications were being made for irrigation consents that could affect native fish habitats, Sage said.

She had also asked for advice about how to improve the conservation of native fish.

"There is work to be done and I hope to make an announcement in the next three months or so."