Authorities have collected samples for testing while Moyne Shire Council is investigating potential lighting factors after more than 50 shearwaters were found dead in Port Fairy on Sunday.
A Department of Environment, Land, Water and Planning spokeswoman said a cause of death was yet to be determined.
"Around 50 short-tailed shearwaters were found dead at Griffiths Island yesterday," she said.
"The cause of the deaths isn't known. DELWP officers have collected a sample of the birds for assessment."
It's believed the bodies are those of fledglings as short-tailed shearwaters are a migratory species and the mature ones have already left the colony.
Only juvenile birds would remain and the spokeswoman said factors including hunger, poor weather and artificial lighting could be affecting their migration.
In the meantime, a Moyne Shire Council spokesperson said officers were working closely with authorities to manage some of those factors.
"Council continues to work with authorities around the annual departure of shearwaters from Port Fairy and the reported deaths of birds over the weekend," he said.
"It's understood artificial light may have an impact on the fledglings. As such Council has taken steps to reduce artificial light in the area around Griffiths Island.
"The light in the rotunda at the entrance to the island causeway will be switched off until after the fledglings have migrated.
"Council is investigating if other lighting in the area can be lowered or switched off during fledging, while still ensuring safety of the public.
"Council will continue to work with other authorities to help the young shearwaters successfully begin their migration."
A similar number of dead shearwaters were found between the breakwater and the Warrnambool Surf Life Saving Club in 2009 due to a fish shortage, while foxes were blamed for a kill on Griffiths Island in 2012.
More recently, it's believed ravens were also contributing to shearwater deaths on the island.
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