A 12-metre whale that became stranded in shallow waters at Lakes Entrance is heading back out to sea.

The adolescent southern right whale was spotted by a charter boat operator on Friday morning west of Lakes Entrance.

It was about 15 metres offshore and rescue crews put a one-kilometre exclusion zone around it to monitor its movements and keep the public at bay.

On Sunday morning, the whale moved to the edge of the town of Lakes Entrance, swimming freely.

Rescue crews in boats tried and guide it towards the entrance, and just before 8am, the whale swam through the entrance and headed to sea.

AAP