An endangered leatherback sea turtle has been sighted by researchers in Melbourne's Port Phillip Bay just a few kilometres from the shore.

Dr Matt Koopman, who saw the turtle while conducting unrelated research on Wednesday afternoon, said it was the first time he had encountered one in 30 years of diving in Victoria.

"We were in a boat going from Hobsons Bay down to Long Reef and the skipper spotted it as we were going along," Dr Koopman said.

"He pulled the boat up, the turtle was swimming towards us and it got to within maybe five metres of us, stuck its head out of the water, had a look at us and then swum away."

Dr Koopman said they were just two or three kilometres from the shore at the time.

"We were fairly close to the cargo ships, they were definitely in sight and it had come from that direction, so it's quite possible it was swimming up around the ships," he said.

"I was pretty surprised ... I never expected to see one, I knew that they did occur in offshore waters of Victoria, but never expected to see one in Port Phillip Bay."

'Pretty rare' for Port Phillip Bay

Turtle researcher at James Cook University, Associate Professor Mark Hamman, said it was rare to see a leatherback in such a high-use area.

"It is an endangered species, it's one of the rarer species in Australia, there's no more nesting on the east coast of Australia and the leatherback turtle in the Pacific Ocean is particularly of concern," Associate Professor Hamann said.

"We do know that the population across the whole of the Pacific Ocean have been declining quite dramatically over the last 10 to 15 years, but putting an actual number on how many are left, is exceedingly hard.

"There's probably in order of 100-odd records south of Sydney, down Victoria, Tasmania into South Australia over the last 10 years.

"It's pretty rare to get a picture and pretty rare for them to actually be inside of Port Phillip Bay, usually ... they'd be out where the jellyfish are abundant."

Associate Professor Hamann said the turtle probably found its way into the bay on the ocean's currents or chasing jellyfish.

"The passage is quite narrow, but these guys are good navigators and it should be able to make its way out," he said.

Turtle sighting 'gives hope' for species

The turtle was about 1.2 metres across and two metres long, Dr Koopman said.

He added he did not initially realise what a great find it was.

"The boys suggested I put it on ... a website for recording and logging unusual sightings," he said.

"So I did that, and we emailed it around to a few people, and it turns out there's quite a bit of interest in it."

He said he had since been contacted by turtle researchers and government departments about the sighting.

Associate Professor Hamann said the sighting was a good sign for the endangered animal.

"It's really good, and it gives us a lot of hope that we're starting to see these animals in southern Australia and the other thing that gives us hope is that people are starting to recognise that it is unique and they let people know," he said.

"To see people giving photos and telling us information - all the data helps us to understand the species better."

He urged others working in and around the bay to keep a look out for the turtle.

"If people do see it, get onto social media, or onto turtle people and share their sightings," he said.

"The more we can start to see these animals and get them recorded the better we'll be at trying to conserve them."