Lachlan Jones, of Gore, was found dead in the Southland town's oxidation ponds in January 2019 and police stated at the time that it was a tragic accidental drowning.
WorkSafe laid a charge against the council under the Health and Safety at Work Act 2015.
The council pleaded not guilty to that charge and a defended hearing was set to go ahead early next year.
However, the charge has been amended by WorkSafe - the allegation that a serious risk of death arose from the council’s alleged breach was removed.
Gore District Council chief executive Stephen Parry said as a result, the council has entered a plea of guilty to the reduced charge of failing to perform a duty.
“As always, our thoughts continue to remain with Lachlan’s whanau. His death was a tragedy," Mr Parry said.
No further comment would be made while the matter remained before the court.