The creek has caused problems for downstream residential property owners during large-scale flooding, such as in 1999 and 2003.
The ORC wants to correct a pair of culvert drains on Stoney Creek to allow for better water flows during occurrences of large-scale flooding.
However, landowners Owen and Eric Hopgood refuse to let the work go ahead.
They claim the redesigned culvert - and entry to their farm operations - will not allow for the safe access of stock trucks and heavy vehicles.
ORC environmental engineering and hazards director Gavin Palmer said the parties had been in dispute for more than three years.
The council felt it had had no other option than to take legal action to ensure the flood mitigation works are carried out.
Statutory remedies were available to local authorities to deal with a situation when a landowner's refusal to co-operate impacts on the risks faced by the rest of the community, he said.
Taking legal action was a last resort because it was expensive to the community, very lengthy, and the hazard still remained in the interim, Mr Palmer said.
"We can't proceed in the way we would like to and would prefer to undertake the mitigation works with their permission," he said.
The Hopgood brothers could not be contacted by the Otago Daily Times last week.
Their lawyer, Dunedin-based Michael Nidd, said he had not received any instructions from his clients on the matter for some time.
To his knowledge, there had been no development regarding the discussions between the Hopgoods and the ORC
