Regional council pollution prevention manager Nick Zaman said the matter was before the court and they could not make any comments.
However, the regional council's abatement notice said nitrogen levels were in excess of the council's resource consent limit of 30 tonnes. It said the average annual sewage nitrogen loading up to February 2012 was 41.5 tonnes.
In a regional council report prepared in February by Mr Zaman, it stated the district council had also been issued with an abatement notice in June 2011 but the requirements were satisfied by the due date of November 30, 2011.
In the report's executive summary the Puarenga Stream was classed as poor for recreational use and not suitable for swimming. It also found elevated levels of faecal coliform occur in the stream during runoff from rainfall.
Rotorua District Council group manager infrastructure services Nico Claassen said because they did not believe the abatement notice represented fair or realistic action by the regional council they had filed an appeal against the notice.
"In the meantime we have also applied for a stay which would effectively put the abatement notice on hold while the appeal process takes its due course."
Mr Claassen said they were puzzled by the latest abatement notice to reduce wastewater derived nitrogen in the Waipa Stream to levels for which no technology exists.
Mr Claassen said the regional council was well aware Rotorua ratepayers had recently invested $8.5 million to upgrade the city's wastewater treatment plant, including installation of state-of-the-art membrane bio reactor technology usually used to treat drinking water.
"That new technology was only made operational last week at the treatment plant and already there are early positive signs that it will extract significantly higher amounts of nitrogen from wastewater."
The matter will be dealt with by the Environment Court which can confirm or dismiss an abatement notice.
Tuhourangi Tribal Authority chairman Wally Lee was aware of the abatement notice but was surprised the matter would be going to court. He did not want to comment.
Last night, a hui-a-iwi was held at Te Pakira Marae, Whakarewarewa.
Mr Lee said the aim of the hui was to gather the stories of iwi who lived alongside the Puarenga Stream for a cultural impact report. Mr Lee said he was preparing the report for the regional council.
"What needs to be understood by the wider public is the devastating cultural impacts the pollution issues are having on our stream."