But NRC said consents could not be transferred and a new one was needed.
NRC has now applied to the same court for an enforcement order against Mr Waldron, group manager regulatory service Colin Dall confirmed.
Principal Environment Court judge Laurie Newhook said NRC failed to provide evidence Mr Waldron's actions caused immediate health risks or contaminated the environment as defined in the Resource Management Act.
NRC also did not think about unintended consequences such as septic tanks overflowing during the busy holiday season if Mr Waldron was unable to continue his operation, he said in his ruling.
Judge Newhook said NRC's concern was more that land on which sewage was being discharged was classified as hazardous activities and industries list (HAIL) land.
That classification means soil on such land should not be disturbed or removed without authorisation.
However, NRC did not provide evidence to show there was any imminent threat by anyone to disturb or remove soil on any land on which Mr Waldron has been conducting his operation.
The judge said NRC has not pursued matters as diligently as one would have expected if it perceived urgent health risks for landowners or the community from Mr Waldron's business.
"I do not want to create the impression that people can flout regional or district plan rules, environment standards or regulations, and expect that the court might turn a blind eye or refuse to grant a council relief," Judge Newhook said.
"The sole reason for refusing an order is that urgency has not been made out."
Mr Dall admitted it took NRC time to act but said that was because his staff tried to work with Mr Waldron and have the site authorised and consented.
"The council is concerned that if Mr Waldron discharges septic tank waste on to a new site, then that site is likely to become a contaminated or HAIL site," he said.
The Northland District Health Board was investigating the sewage disposal pond after a public complaint and the Ministry for Primary Industries was also involved after reports of vegetables irrigated by the pond overflow being sold.
Mr Waldron denied using overflow to spray vegetables. He had said he was not operating illegally and was prepared to go to court over the matter.