Emergency works have been carried out at the wastewater ponds at Franz Josef Glacier - which were completely submerged last month when the Waiho (Waiau) River burst its banks causing extensiveflooding north of the resort.
Close to 2m of water went through the Scenic Hotel at Franz Josef, forcing the evacuation of close to 200 people.
Raw sewage from the Westland District Council ponds was still flowing straight into the river days after the March 23 event.
Council district assets manager Vivek Goel said its contractor, Westroads, had been instructed to do "minimum" works at the ponds to control the discharge of wastewater.
A broken section of the effluent intake pipe at one pond and damaged bund at the northern end of the other had now been reinstated.
However, it could take up to four months to have pond one working effectively.
Mr Goel said the ponds - which are hoped to be fully rebuilt in a new location to the tune of $6.1 million in the not too distant future - were "very badly damaged".
"The ponds at this stage have been exposed to severe flooding resulting in pond one silted with river sand and gravel. It will take more than four months before any reasonable treatment could be achieved for the incoming wastewater.
"The situation has been advised to the West Coast Regional Council and we are in the process of working on an alternate treatment process to be established at a new site in Franz."
Westland Mayor Mike Havill said the ponds were still non-compliant but discharge was no longer going straight into the river.
"The ponds were non-compliant before the event and they are still non-compliant now," the mayor said.
"The important bit is there's no risk to public health and safety and we will have primary treatments in place."
The new wastewater infrastructure is included in the council's draft annual plan.
Franz Josef residents could face increased targeted rates to cover $3 million of the cost while a Government subsidy for the remainder is being sought.
Mr Goel could not give an estimate on the cost of the recent emergency works.
