Warrnambool Coast Care Landcare Network penguin co-ordinator Trish Corbett said the group had counted five breeding pairs on the island on Thursday.

It follows the death of 15 male breeding penguins earlier this year, when foxes reached the island before maremma dogs were posted to guard the penguins.

Dr Corbett had feared there would be no further breeding penguins this year.

"We weren't sure if there were any breeding penguins at all," she said. "We lost a significant number of our breeding males."

Population numbers had been recovering after foxes also reached the island in August 2017 and killed about 70 breeding penguins.

"With that one big kill and one smaller kill it has almost decimated the population again," Dr Corbett said.

She said numbers had been down compared to the 180 breeding penguins on the island in 2016, and penguins were also arriving at unusual times.

Researchers expect the breeding season to be between October and February, but small numbers of penguins have been arriving as early as June and others later in the season like those seen this week.

"We don't know why they are late, or if the whole season will be shifted back now," Dr Corbett, a researcher at Deakin University, said.

"We think this is all linked in with climate change, with penguins arriving at unusual times."

Birdwatches also observed the late arrival of short-tailed shearwater birds at Port Fairy earlier this year, but Dr Corbett said it was unclear if the two events were related.

Have you signed up to The Standard's daily newsletter and breaking news emails? You can register below and make sure you are up to date with everything that's happening in the south-west.