Warrnambool Coast Guard spotted the leatherback turtle during an exercise on the water on Sunday.

Commander Allan Wood said the turtle was heavily tangled in a line securing a Deakin University buoy.

"The rescue process was extremely difficult and focussed on the welfare of the turtle and safety of attending crews," Mr Wood said.

He said with the sea swelling to two metres and unsuccessful attempts to rescue the turtle, reinforcements were called in with Port Fairy Surf Life Saving Club attending.

"The turtle was enveloped in a net and cut from the buoy line and secured to the inflatable rescue boat,"Mr Wood said.

He said once in shallow waters, the rescue crew dragged the turtle to the beach.

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He said the turtle was estimated to be two-metres long, one-metre wide and weighed more than 400 kilograms.

They were assisted by Port Fairy Marine Rescue Service, Port Fairy Surf Life Saving Club and Melbourne Zoo.

Port Fairy Surf Life Saving Club chief training officer Shaun Murrihy said the club was previously involved with the rescue of whales and seals.

"We have this amazing system of personnel equipped to rescue our marine creatures," he said. "It is great we have the personnel and the equipment to do all this."

Melbourne Zoo marine response unit officer Ebony McIntosh said the turtle was suffering from deep cutting wounds to its flippers, abrasions to its shell and exhaustion.

"The turtle was brought to shore and because of its injuries and inability to swim and dive normally it was transported to Melbourne Zoo for assessment on Monday," she said.

"Melbourne Zoo and Sea Life Melbourne Aquarium veterinarians inspected and treated the turtle at Melbourne Zoo, but it passed away overnight."

Deakin University's Marine Science team manage a network of wave buoys funded by the Department of Environment, Land, Water and Planning to monitor coastal erosion.

Marine Science Associate Professor Dan Ierodiaconou said the incident was the first of its kind.

"We're grateful to Melbourne Zoo's rescue team for their efforts in caring for the turtle," he said.

"We've informed DELWP who will look in to how this happened."

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