EPA officers tested the water quality after a member of the public reported the dead animals.
Acting metropolitan manager Danny Childs said wildlife deaths weren’t always caused by pollution.
“EPA officers found no evidence of pollution at the beach, so we believe these deaths were most likely due to natural causes,” he said.
“Fish and penguin deaths can occur due to range of factors including changes in water temperature and weather conditions, which may have occurred here.
“This community member did the right thing – prompt reporting increases our ability to identify whether a pollution event has occurred and helps EPA minimise any environmental harm.”
In August, 2014, 30 little penguins washed ashore at Altona beach and an investigation found they had become caught in a commercial fishing net.
The Department of Environment and Primary Industries interviewed a fisherman operating in the area after he was reported by a member of the public.
No enforcement action was taken as the deaths were deemed accidental.
People can make a report to the EPA by calling 1300 EPA VIC (1300 372 842) or via its website.