ECan has said it would cost $1.7 million to convene, research, prepare and conduct hearings for 32 applicants, members of the Upper Waitaki Applicants Group (Uwag), who sought 61 consents and another 51 ancillary consent applications.
Uwag spokesman Barry Shepherd said each consent would cost the applicant $15,678.78 and each ancillary consent $4688.15 for a total of $1.2 million.
An extra $500,000 would be levied based on the amount of information Ecan needed to collect on each application.
It was going to cost one farmer $34,000 for ECan to consider four consents, including one that has operated for 40 years.
Initially, the Mackenzie Basin farmer was seeking to renew a water take consent at 57 litres a second and maintain a weir, along with two others, for the provision of stock water and the return of excess water to a waterway.
It cost the farmer $25,000 to prepare his case, but when he learnt of the cost he opted to abandon the two stock water applications.
Mr Shepherd said preparing their consent applications was costing farmers $330 a hectare and while some farmers had reduced the number of applications, they had few choices but to pay the Ecan rates.
They were concerned there was no peer review to prove the costs were justified or could be substantiated.
He said ECan staff travelled from Christchurch to see applicants rather than using staff from its Timaru office, turning a one-day trip into two.
In many cases the applications were for small areas of 200ha to ensure they had winter feed.
Mr Shepherd said Uwag represented 29% of the total Mackenzie area but 72% of those seeking resource consent, with the rest of the applicants processing their own applications.
In late July, ECan established the cost for the Uwag applications which were initially to be heard by three commissioners.
Mr Shepherd said the number of commissioners was increased to four at the suggestion of Cr Eugenie Sage, who felt Maori issues needed to be represented.
Edward Ellison was then appointed.
Council minutes show such a motion was moved by Cr Sage and seconded by Cr Rik Tindall.
It was carried six to five, with two absent.
Mr Shepherd said his group was not opposed to Mr Ellison or his role, but rather the cost of having a fourth hearing commissioner.
Waitaki member of Parliament Jacqui Dean said she had raised concerns about the performance of ECan, the cost and time taken to renew water consents, with the Ministers of the Environment and Local Government.
"It seems to me the process is too expensive and too bureaucratic given these are consent renewals," she said.
Mrs Dean said similar concerns were raised by other South Island MPs and mayors and recently the Government announced a review of ECan's performance.
She has visited and discussed issues with leaders of regional councils around New Zealand but requests to meet ECan had been rejected.
"I haven't seen a council [ECan] that has been particularly willing to engage."
She hoped that would change, with a meeting planned with new ECan chairman Alec Neill at which she will invite him to meet farmers in the Upper Waitaki catchment to hear their complaints and grievances.
Mrs Dean said she wanted to ensure ECan was working within the legal framework of the Resource Management Act and that it worked for both the applicants and the council.