Voluntary compliance by the majority could be undermined by the minority who did not comply, he said.
Federated Farmers senior policy adviser Richard Gardner said the federation favoured "best practice" guidelines on how councils exercised their duties under the RMA if they brought common sense and consistency to the role.
But there was concern the new guidelines missed opportunities for fairer outcomes, he said.
Too often, Federated Farmers found councils were misusing their power under the legislation and managing compliance and enforcement matters inappropriately.
The guidelines would hopefully usher in more practicality and consistency to the exercise of that role.
Federated Farmers found fault with some of the guidelines and was disappointed it had not been more involved in putting them together, Mr Gardner said.
There was concern about the lack of differentiation in the guidelines between routine inspections and inspections arising as a result of a complaint.
The federation also saw faults in the way enforcement decisions were handled.
"We have long held the view there should be a pecuniary regime for 'misdemeanour' and accidental offences, and criminal prosecutions reserved for the worst, deliberate offences."
The current strict liability standard regarding those prosecutions should be removed, he said.
The responsibility for criminal prosecutions should be removed from local authorities to the police or the Environmental Protection Authority.
Federated Farmers would welcome the opportunity to be more involved in the review of the RMA and related matters, such as the guidelines, Mr Gardner said.
Mr Parker said although the RMA allowed for a tailored and localised approach to CME, there were models and principles of best practice that could be adapted to suit local circumstances.
The purpose of the guidelines was to clarify what best practice looked like by providing guidance and support for frontline staff through standard tools and templates.
National Monitoring System data showed 14% of resource consents monitored by all councils in 2015-16 were non-compliant. For regional councils, the figure was 20%.
The Ministry for the Environment was establishing a new unit to oversee compliance with the Act and to improve consistency across councils, Mr Parker said.
At a glance
The purpose of the guidelines is to:
• Strengthen compliance, monitoring and enforcement (CME) capability and improve rates of compliance by clarifying what best practice looks like.
• Advise councils on how to strategically approach CME functions.
• Emphasise the importance of CME as a set of functions, and of robust CME processes.
• Provide greater transparency and accountability for CME.
• Support council officers undertaking CME by providing standard tools and templates.
