Damage to the stream appears to have been limited after a quick response by the Dunedin City Council, but the final outcome now awaits an investigation by the Otago Regional Council.
City council network manager Rezaul Haque said the council was called about the spill at 9.08am, a crew was on site at 9.30am, and the overflow stopped at 10.10am.
The blockage, near Kaikorai Valley College, was caused by roots growing near the pipe, which caused a buildup of debris, probably exacerbated by recent rain.
It was not possible to measure how much sewage escaped, but the council crew had gone down the stream to clean it up after the blockage was stopped.
It was not unusual to find roots in the sewerage system, Mr Haque said.
"The Dunedin system is quite old."
Regional council environmental services manager Martin King said an investigation would be carried out, the possible outcomes being anything from "do nothing, through to prosecution".
Some raw sewage had been in the overflow, but staff had taken samples after the cleanup, and the stream was "fine", Mr King said.
City council water and waste services manager John Mackie said root mats could grow undetected, and the problem was one the council was focusing on.
There were plans for more work with CCTV cameras to deal with the problem.
