The dead mammals, one of which was badly decomposed, were removed from a beach a few kilometres from the town of Mallacoota on Thursday afternoon.

A front-end loader carried the carcasses up the beach to Bastion Point before being put on a truck to be transported to another site where they will be buried on Friday, the Department of Environment, Land, Water and Planning said.

The duo had been discovered and reported to authorities earlier in the day.

"We wanted to remove the carcasses from the beach as they were very close to the Mallacoota township, the odour could have been very strong, and there are hazards associated with contacting carcasses," incident controller Stephen Young said.

"The beach is regularly used by locals and visitors so by removing the whales the beach can be enjoyed again."

It is not known if the two deaths were related to the 27 pilot whales which mysteriously stranded themselves at Croajingolong National Park in East Gippsland.

The mammals were found on Tuesday with a humpback whale, which was understood to have died in a separate incident, but washed up on the same shore.

A team of specialists returned to the national park site on Thursday to carry out tests on the four remaining carcasses, before leaving them to rot.

A shark warning has been issued for the area, amid concerns sharks could be attracted to the shores.

Due to the remote location, burial or removal of the whales is not feasible, according to the environment department.

Australian Associated Press