Mr Holmes said the amount council wanted to spend on the transfer was "overkill" and questioned how many eels were actually living in the ponds.
"I'm not saying the figure's right or it's wrong, but they don't know how many eels that are there."
He also questioned why council was taking such an interest, as a few years ago sewage was discharged into the Ruamahanga river and a lot of eels died as a result.
"Council were responsible but walked away - dead eels were everywhere and no one would admit liability," he said.
"Why should we spend all this money now."
Mr Holmes said most eels would find their own way to the new ponds anyway.
"I don't want us to be spending a lot of money on it," said Mr Holmes.
"The reality is we don't know how many eels there are."
"As much as I agree with what they're going to do, I think it's an over-reaction."
Chief executive Wes ten Hove said the incident was part of the evaluation work undertaken a few years ago to determine the optimum wastewater treatment plant upgrade solution at Homebush.
Work was done to investigate the option of retaining the existing ponds.
"Part of this investigation work involved lowering the level of the ponds by pumping treated effluent out of the ponds.
"Flow passed through an existing grate that inadvertently caused a number of eels living in the ponds to be injured or killed," he said.
Council is working with two local iwi on the initiative and is exploring funding options.