Council authorised the $165,000 spend at a council meeting on Wednesday.
Last month heavy rain inundated the Omakau Wastewater Treatment Plant next to the Manuherikia River for about 24 hours, extensively damaging the embankments with tree debris, silt, gravel and floodwater entering the two treatment ponds.
Wastewater also spilled into the Manuherikia River.
Record or near-record rainfall was documented at several weather stations in Central Otago with water supplies in Naseby, Ranfurly, and in particular Omakau affected, resulting in a boil water notice for Omakau and Ophir for two weeks.
CODC Three Waters director Julie Muir said given the severity of the event, Council got away "relatively lightly" in terms of damage to the site and she agreed with comments that the Council, community and the plant had "dodged a bullet".
There was no "quick fix" to the problem and work on long-term solutions was under way.
Council staff were working to identify a new treatment site and options for discharge to land instead of to water.
Councillor Tracy Paterson said there had been good communication to the community during the event and it would be important to keep this up.
Councillor Stu Duncan expressed his frustration the emergency event reserve was available for repairs to the wastewater treatment plant but had not been an option when bridges in the Maniototo had been damaged in flooding last year.
