Dunedin City Council Three Waters group manager David Ward said heavy rain over the past week meant partially treated wastewater had been discharged into the sea.
The wet weather caused a large amount of stormwater to discharge into the sea, Mr Ward said.
Some also entered the Tahuna wastewater treatment plant and the effects of this were now being seen at Tomahawk Beach.
While the risk of contamination was considered to be low, the beaches would be tested daily.
The Otago Regional Council and Public Health South had been notified and signs were up at the beach.
A precautionary approach was recommended.
Swimmers, surfers and shellfish gatherers were being urged to avoid the water at Tomahawk Beach.
Dog walkers were encouraged to not let their animals into the water.
"Obviously there are health risks associated with partially treated wastewater so we need people to stay clear of the water at Tomahawk at the moment," Mr Ward said.
The council was doing its best to ensure the beach returned to its usual status, Mr Ward said.
