"It's looking a little marginal, or even more than that," he said.
Late last week council officers revealed 15 per cent of the planned irrigation area cannot be built "cost effectively" because groundwater levels were higher than had been anticipated when the old ponds were decommissioned.
Mr Holmes said one old pond - known as Pond 3 - will never be able to be drained.
He said an option open to council was to revert back to an idea which had emerged years ago.
"That is to store the treated wastewater and then sell it to farmers for irrigating cropping land. That's the only way we will get it out of the river," he said.
The construction costs of the project, let to Hopper Construction, was for $32 million but between 1999 and 2010 further expenditure of $14 million was split between buying land ($6.4 million), plant upgrades including extra bunds in Pond 3 and investigation, design and resource consent costs
In the wake of comments made by Mr Holmes this week Mr Borren said the $14 million was always separate from the Hoppers Construction fixed contract and any councillor who wanted to access that information could have done so at any time.
Both Mr Borren and council engineer Ian Steer are satisfied that apart from the glitch over the reduced irrigation area affected by excessive groundwater the project is on target and the border dykes now in commission are working well.
Mr Steer said it was always intended to disperse no more than 30-40 per cent of treated effluent to land.
The remainder would be stored with the intention of releasing it into the river only at times of high flow.
He said the figures quoted by Mr Holmes regarding last summer's dispersal of treated effluent to land would not truly reflect what would happen in future when further tests had been done on border dyke performances and when the plant if fully commissioned.
According to the report prepared by Mr Paris $1.25 million has been allowed in the 2014/15 Annual Plan to complete the project.
Mr Paris has reported as at the end of last month outstanding debt funding for the Homebush project stood at $39.9 million.
Several councillors spoken to expressed surprise at learning the cost of the scheme to date but all, including Mr Holmes, said Mr Borren, who has only been in the chief executive role for two months, had made it clear he wanted " transparency" on this and other issues and they were confident that would be so.