The Amalgamated Workers Union, which represented staff in the council's water and wastewater department before maintenance was outsourced in 2014, says there was no plan in place and the council mismanaged a number of "choke points'', which exacerbated flooding.
Group manager water and waste Dr Laura McElhone strongly disputed the accusations and said union representative Steve Scandrett was guilty of "throwing about unsubstantiated guesses to stir''.
However, she accepted that in future flood events the council would look at bypassing the Tahuna wastewater treatment plant, which would have made some difference if it was done during last June's floods.
Mr Scandrett told the Otago Daily Times the union's accusations were based on information it had received from people with experience in the water and wastewater sector, including current council staff.
This information made it clear councillors and the mayor were "still being misinformed by their own staff''.
"Since 2014 the water department had no plan in place to counter potential flooding and to lay the blame on Fulton Hogan is a convenience, especially since they drew shortcomings to council's attention to problems several months before the flood,''
"It would appear that the city council still don't know what caused the flooding or its managers are still hiding the truth,'' Mr Scandrett said.
The failure to divert the city's foul sewage, which was 90% to 95% stormwater at the peak of the floods, into the ocean was among the unreported mistakes which exacerbated flooding.
There was also a failure to divert foul sewage from the hill suburbs down Kaikorai Stream and the sewage system was so inundated with water, manhole covers blew into the air and sewage escaped into the streets.
Mr Scandrett also pointed to issues caused by the "new management'' system put in place after maintenance of the water and wastewater network was outsourced.
The system meant "minor works'' were completed before staff visited Portobello Rd pumping station at 10am, which became blocked and contributed to the flooding.
There was no provision for the emergency clearing of grates, including the one at the Portobello Rd pumping station.
Emergency clearing of grates would have been done before outsourcing in 2014 as the "golden rule'' staff had before extreme weather events was to "clean the grates or there will be flooding''.
Dr McElhone accepted that bypassing the Tahuna wastewater treatment plant and sending foul sewage straight out to sea at Lawyers Head would have made a difference.
It was only once floodwaters receded that council staff considered the option, which would have breached the council's resource consent with the Otago Regional Council.
"It would have made a difference, there is no question, but it might not have actually helped South Dunedin a great deal.
"It might have taken pressure off other places.''
In future events of a similar magnitude it would be considered earlier, Dr McElhone said.
"We now have protocols in place so that this is considered earlier and can be fast-tracked if necessary.''
There was no loss of knowledge when maintenance of the water and wastewater network was outsourced as all but one staff member was either picked up by City Care or stayed employed at the council.
The screen at the Portobello Rd pumping station, which is now being replaced after its design was found to have contributed to flooding, was cleaned on the Friday before the flood, as was routine.
Staff did not prioritise "minor works'' over visiting the Portobello Rd pumping station and instead went to other urgent call-outs, "including calls to flooding''.
There was a rumour that a City Care staff member's call to go to the Portobello Rd pumping station was "ignored'', but this was unsubstantiated, and it was unclear what difference it would have made had such action been taken.
