The Department of Environment, Land, Water and Planning Barwon South West region says the calf's mother, a well-known whale and regular visitor to Logans Beach whale nursery called Tripod, arrived in Warrnambool in late June with her calf, stayed for three days and left.

DELWP said on its Facebook page Tripod returned to the area earlier this month, however her calf has not been sighted.

"As a calf is completely dependent on its mother within the first year of its life, we suspect the calf has died while the pair were away from Logans Beach," the post said.

"Photographs taken by citizen scientist show unusual marks on the calf's flanks. At this stage, we are not sure of the origins of the marks however they may have been caused by an attack from a predator or by an interaction with a boat.

"Although we haven't confirmed how the calf died, the incident highlights the vulnerability of the critically endangered species.

"It's important that water users remain vigilant for the presence of whales and be are aware of the rules in place to protect them."

The Logans Beach exclusion zone is in place between June and October every year, preventing powered vessels from entering the area to limit disturbance to whales and their calves.

Outside of the Logans Beach exclusion zone, the following minimum approach distances apply:

Anyone who observes breaches of the minimum distance requirements is urged to note details and report the offence immediately to Barwon South West Forest and Wildlife Officers via the DELWP Customer Contact Centre on 136 186.