The spokeswoman said the overflow was located close to Rata St.
The blockage, however, was located near Puriri St and Tawa St. Contractors were able to locate and clear the blockage by 9.30pm. Clean up of the overflow area took another 30 minutes, the spokeswoman said.
The blockage was caused by a build-up of fats and wipes.
Signage was placed along the beach earlier today warning people to stay out of the water.
The council also conducted testing of the water for health risks.
The warning signs will be removed from the beach once the tests confirm the water poses no health risk. The results of the testing won't be known until later on Tuesday.
The spokeswoman said there was a potential risk to people of contact with bacteria from sewage that could lead to infections of the gastrointestinal tract and skin, eye and ear infections, plus breathing difficulties.
Follow-up testing will take place tomorrow morning and the test results are expected on Wednesday.
"There are unlikely to be any long-term risks associated with the overflow. Pilot Bay is a highly dynamic environment, water is well mixed and quickly refreshed," she said.
"We acknowledge that any discharge of this nature is distressing to tangata whenua and the wider community.
"It is important that we continue to raise community awareness about the impacts of putting fats, oils, grease and wipes into the wastewater network, to minimise the number of overflows we see in the city," she said.
The council was unable to estimate the volume of the overflow.
When wipes mix with fats and oils from dishwashing, they form blockages such as this example, the spokeswoman said.
"Overflows come at the expense of our community and our environment and are not a good look for visitors to our area."
These sorts of blockages are also known as fatbergs and have been the cause of closures at Pilot Bay and around New Zealand in the past.
The council will run its third Save Our Pipes From Our Wipes campaign this summer, aiming to discourage people from putting wet wipes down the loo - even those brands that claim to be "flushable".
