EPA south west regional manager Carolyn Francis confirmed the authority was "investigating the source of the material and will take the necessary actions to require clean-up and prevent future events".

Volunteers said they cleared hundreds of the balls, which included congealed oils, grease and hairs, from Shelly Beach on the weekend.

They found the materials on shorelines near an outfall of the Warrnambool Waste Treatment Plant, but Wannon Water rejected the volunteers' claims that material had recently come from the plant.

"While some fat balls have been released from the plant historically, we are confident that fat balls have not been released in recent times," managing director Andrew Jeffers said.

The water authority in 2017 installed screens to prevent solid materials flowing into the ocean and Mr Jeffers said they had worked "as designed".

He said Wannon Water was not notified of the presence of fat balls on the beach last weekend and "therefore, were unable to assist with the clean-up".

"We did become aware of social media posts on Sunday and we immediately responded by organising an inspection of the beach that morning, which found only minimal evidence of small fat ball fragments," Mr Jeffers said.

"On Monday morning we also proactively notified the EPA and DELWP of the situation."

Good Nurdle Hunting volunteer Colleen Hughson said she had monthly correspondence with the EPA about waste on the beach and believed an investigation would unlikely resolve the issue.

"We have had two years of ongoing issues," Ms Hughson said.

She said she believed licensing issues had prevented the EPA from intervening in the past.

Ms Hughson rejected that the material was historical. "We feel we have removed the majority of the historical waste now ... there's no way it has lasted in the ocean for two years," she said.

A Victorian government spokeswoman said the government would "await the outcome of the EPA investigation" before commenting further.

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