The Government's plan to clean up New Zealand's water has raised fear and major concern for Southland farmers.

The Ministry for the Environment hosted two public meetings in Southland about the proposed changes.

However, it underestimated farmer attendance.

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At both events - one held at the Civic Theatre in Invercargill on Wednesday and another at the Winton Bridge Club on Thursday last week - hundreds of people listened to the presentation through speakers outside the venue.

Farmer Warren McPherson sat outside at the Winton event.

"I'm glad that it is not raining. It's a bit disappointing ... They did not listen to the farmers before doing this plan, they gave us a very short period of time for consultation and now we have hundreds of farmers with questions and concerns."

A Ministry for the Environment spokeswoman said the ministry had not anticipated the attendance and had looked for venues with a 200-person capacity.

"We have learnt from these meetings and will definitely have another in Southland soon."

Both events explored five topics of the Government's policy: freshwater quality, urban development, land use, hazardous waste disposal, and waste minimisation.

However the National Policy Statement on Freshwater was the main subject of discussion.

McPherson believed the plan targeted only farmers.

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"It is not fair the water quality issues be blamed only on dairy farmers ... They want the farmers to clean something that isn't necessarily their fault."

Ministry for the Environment's director of water Martin Workman acknowledged most farmers were doing a good job but water quality was "in trouble".

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An Invercargill attendee said six weeks was not enough time for consultation.

"You don't know the amount of stress you've put on everyone here," he said.

Waiau Rivercare Group member Claire Jordan said the national policy would have severe consequences for the catchment.

Agribusiness consultant Deane Carson questioned the plan's proposal for a maximum contaminant level of 1 mg/L for nitrite-nitrogen in water bodies.

He asked what the Government had done to measure the impact of these limits nationwide.

New Zealand Ministry for Primary Industries adviser Darran Austin said the Government had "not realised any" - and the audience responded.

"It's quite concerning to actually get this proposal to us without any economic modelling," Carson said.

The farmers called for Environment Minister David Parker to "come down and listen" to them.

The public consultation will continue for three weeks and public submissions close on October 17.