Mr Allen said the council was still waiting for the report outlining the results of the investigation which could be two to three weeks away.
"We are a little bit surprised they have had an investigation and we have not had the findings of that investigation."
Waikato Regional Council chief executive Bob Laing said the council was reviewing its processes as a result of the council's criticism of how the city council was informed of the prosecution.
However, city councillor Roger Hennebry said he had been told from a regional councillor they had lodged three prior complaints about sewage going into the river before prosecuting. Mr Hennebry's wife, Jane Hennebry, is a regional councillor.
"I'm actually appalled at it and I'm appalled because Waikato Regional Council over three months had given our council three warnings about an issue which they perceived to be ignored."
It is understood the issue began in June 2011 and the city council employed a consultant to address the problem.
City councillor Dave Macpherson also criticised the communication between the two local government entities. He said a senior councillor at the regional council had told him the city council had been fully informed of the prosecution but he believed that was not the case.
City councillor John Gower raised concerns about the processes between the two councils and objected to a staff member being singled out.
Mr Laing would not comment on past issues at the Pukete plant, the council's reasons for prosecuting over the July spill and for prosecuting a staff member.
Meanwhile, the city council is making changes to its processes, including staff training, as part of the $32 million upgrade to the Pukete wastewater treatment plant.