Central Hawke's Bay Mayor Alex Walker said she was disappointed the council had been charged "over minor exceedances of resource consent limits", but was pleased the charges related to infrastructure the council was already working to address.
"Any failure to comply with consent conditions is obviously a concern to us as a council, and to our community," Ms Walker said.
"It is disappointing that it has got to this point but we are continuing to work closely with the regional council over these issues."
The Waipawa and Waipukurau wastewater plants had been upgraded two years ago to meet new standards required under new resource consents, which came into effect in October 2014.
The CHBDC has been warned previously about exceeding discharge limits, and in March it was reported court action was a possibility if the plants continued to breach consent conditions.
HBRC chief executive Andrew Newman said because the council was a regulator, it had to be consistent in enforcing action when there were breaches of consent conditions.
"If you don't regulate and enforce your regulations consistently then that's not fulfilling the function adequately," he said.
Following the charges for HDC, Mr Newman said there had been commentary in the media about "council versus council".
"The point I'm making is that we have to be consistent with councils and that's exactly what we're doing," he said.
"Over a number of years the [HBRC] has taken a lot of criticism for not holding [CHBDC] to account in terms of the performance of its wastewater pipes, and it is actually doing that.
"We can't have one rule for one [council] and one rule for another."
A court date for these charges is yet to be set.
CHBDC chief executive John Freeman said he believed the charges were in relation to a heavy rain event in September which caused both plants to exceed resource consent limits.
Changes to the Waipawa plant had been in place since September, and compliance with resource consent limits have been achieved since then.
A budget allocation, from the Long Term Plan, of $1.5 million was brought forward earlier this year to add two new ponds in Waipukurau to mitigate the impact of stormwater entering the system.
These ponds were under construction, due to be operating by late March. They were expected to have a large impact on the performance of the whole system.
Hastings Mayor Lawrence Yule said the regional council had been consistent in regard to the prosecution, however "they have been working with the [CHBDC] for over two years on this, and they decided to investigate us and prosecute us three months into a six-month opportunity to do so".