The Healthy Rivers Wai Ora Plan Change 1 is aimed at addressing the water quality by imposing rules and restricting any change on land use over the next 10 years to the rural sector.
The complainant, a North Waikato farmer, told the Herald he was awaiting the council's response and did not want to comment at this early stage.
The Herald understands he is being backed by a group of other land users in the lower Waikato catchment area.
A Waikato Regional Council spokesperson confirmed the council had received notice that an individual made a complaint to the HRC in relation to a policy in the proposed Plan Change 1 and was responding to the complaint.
The council would not comment further, claiming the HRC's dispute resolution process was private and confidential to those involved.
The HRC also confirmed it had received a complaint about the council, but declined to comment further due to the confidential process.
The HRC website states that once a complaint is accepted by the HRC, it tries to resolve the issue through informal methods, including phoning the other party, giving information or through mediation.
If a complaint is not successfully resolved through the HRC's processes it can be escalated to the Human Rights Review Tribunal to rule on the claim.
But a source told the Herald the decision could have a huge impact on the council financially. Any changes could result in iwi withdrawing their approval of the plan and force the council back to the drawing board.
However, another source said it could come down to simply amending the rules to allow all parties in similar circumstances to apply for an exemption to the land use change rule.
At the end of June, the project had cost up to $19.3 million and council has approved further funding in its long-term plan of up to $9m.
Submissions on the plan are due to be heard by a panel of five independent commissioners later this year.
