He believed he was operating within the guidelines and his systems were 100 per cent compliant, but the NRC said consents could not be transferred and a new one was needed.
NRC group manager regulatory service Colin Dall said the council had chosen to take a pragmatic approach to the matter and work with Mr Waldron to regulate his operation at a new site.
Mr Waldron has until September 16 to comply before the council considers taking further action but in the interim he is allowed to continue operating provided there was no overflow from the ponds.
Mr Dall said the council first examined the Child Rd site on August 26, after it had established earlier last month the operation had been moved.
Mr Waldron formally notified the council he was operating from September 4, 2015, and at that time was told to obtain a new consent as the existing one could not be transferred.
"Mr Waldron holds a resource consent for a similar operation at a different property that is no longer operational due to the property being sold," Mr Dall said.
"The operation at Child Rd is a similar scale to previous site and has a low environmental risk. Mr Waldron wanted the council to transfer this consent to new site, but legally this cannot be done."
The next visit to the site by council officials was not until March this year. Mr Dall said if the deadline was not met then action including issuing an abatement notice requiring Mr Waldron to stop, serving an infringement notice or prosecution could be taken.
Mr Waldron said he was not operating illegally and had informed the council of his new site and his plan to transfer the resource consent when he first moved.
"I'm not playing games. I'm very serious about cleaning up Northland and my operation is 100 per cent inside the guidelines," Mr Waldron said, who has 20 years of experience working with septic tanks.
"I can clean our environment up if they [NRC] will work with me and let me. But don't charge me, don't steal my money."
He said he was based on land where there was an "arrangement that everyone was 100 per cent happy with".
"I'm not failing the public, I'm working for them."
Mr Waldron said he had a resource consent and was prepared to go to court over the matter.
Medical officer of health Claire Mills confirmed the health board had received a public complaint about the operation and were working with other agencies on the investigation.
Dr Mills would not comment further.
MPI said it had been contacted by the NRC and now had sufficient information to begin an investigation in conjunction with the council after reports of vegetables irrigated by the pond overflow were being sold.
Mr Waldron denied using overflow to spray vegetables.