GWRC environmental regulation manager Alistair Cross said the company had failed to re-evaluate their compliance needs as the business grew and was still working under the requirements of a much smaller business.
"Henergy has since undertaken a very comprehensive review and upgrade of the site infrastructure and applied for resource consent for future discharges. They have been a pleasure to work with and have since gone beyond meeting compliance requirements to working to best practice standards."
In delivering his decision, Environment Court Judge Thompson noted Henergy's guilty pleas, cooperation, and efforts to come into compliance since the investigation. He considered Henergy to be a socially responsible company.
Henergy managing director and company founder Graeme Napier said the judge noted it was not a punishment against a person, but intended as a deterrent to the industry.
He said Henergy uses a dry effluent system that enables it to transport most of the poultry effluent off-site for lawful disposal.
A small amount remains on equipment in the poultry sheds, and the water used to wash down the equipment is pumped to settling ponds.
He said occasionally Henergy has pumped water from the ponds onto one of its fields where it is discharged to land, but because the water still contained some effluent this occasional pumping should have had a resource consent.
"We were surprised and disappointed when we were told we had breached environmental regulations," said Mr Napier.
"We are acutely aware of the importance of strict environmental regulations in farming industries, but we simply hadn't realised we would need a resource consent to recycle our water in this way".
He said they have since made a "significant capital investment" in new settling ponds and state of the art irrigation systems.
"Henergy is very proud of its long-standing reputation for looking after animals, and a huge part of that is looking after the environment," said Mr Napier.
"We're usually exceeding standards rather than finding out we've inadvertently breached a particular standard. When the council informed us of the issues, we swung into action not only to fix the immediate problem, but also to make an investment plan for the next 15 years so that we can stay at the forefront of sustainable farming.
"Finding out about the issues with the old ponds has reconfirmed to us how important our environmental management systems are and the full review has been a positive and valuable exercise."