In an office up a steep hill in a seaside suburb of Athens, a tiny blue light flickers from a computer terminal. Dr Alexandros Frantzis, Greece’s foremost oceanographer, points it out. The light, he says, tracks marine traffic “in real time”.

It is key to saving one of the world’s most endangered whale populations.

“Every few seconds it logs the position, course and speed of a vessel entering Greek waters,” he says. “And that is vital to mapping shipping densities in areas populated by sperm whales.”

Frantzis has spent nearly a quarter of a century studying marine mammals. His desk, like his small Pelagos Cetacean Research Institute, is testimony to a passion that has helped transform understanding of dolphins, porpoises and whales in a country where little was known about marine life barely two decades ago.

Shelves are stacked high with the bones of sea mammals big and small. The remains of a sperm whale’s lower jaw are propped against a wall in his back office. And in a room beyond, the skeletons of two whales – gargantuan, crusty and yellow – lie neatly assembled across the floor.

“Greece’s marine environment is very rich in species,” says Frantzis. “In antiquity cetaceans were taken very seriously. Aristotle wrote the first scientific study, his Historia Animalium, about them. You could say Greeks are the first and the last to come to the field, which is why urgent measures are being taken.”

Sperm whales are the focus of Frantzis’s latest campaign. Although prevalent in other seas there are fewer than 300 in Greek waters, their largest habitat in the eastern Mediterranean.

Like marine mammals in most places, the whales face a multitude of threats, from entanglement in fishing nets to ingestion of plastic waste.

In Greece there is the added risk of noise pollution from Nato warships conducting underwater sonar drills – exercises blamed for disorienting whales reliant on their own form of sonar to navigate and hunt.

Seismic surveys, following the discovery of underwater hydrocarbons, also pose a threat.

But Frantzis says the biggest danger to local cetaceans is the chance of colliding with a ship. He singles out the waters off the western Peloponnese, an area where whales swarm but one of the busiest routes for tankers, cargo vessels and cruise liners.

Last month a nine-metre whale washed up on a beach in Santorini, the latest in a series of strandings. Frantzis now has a large white bone – one of its teeth – on his desk.

For sperm whales, death by collision is by far the most painful, he claims, with propellers often leaving the animals torn and gashed.

“We don’t know how this latest incident occurred,” he sighs, dispelling reports that huge amounts of plastic had been found in the mammal’s digestive tract. “But what we do know is that at least one whale every year is killed as a result of a ship strike. It’s a death rate the species in these parts cannot survive.”

Conservationists contend that if shipping lanes were routed farther offshore, the risk of ship strikes would drop dramatically.

“Sperm whales like waters off steep underwater gradients but unfortunately the Hellenic trench off the Peloponnese is also the direct route for ships moving parallel to the coast,” the British marine mammal scientist Russell Leaper told the Observer.

“The solution would be to move ships a little bit offshore into deeper waters less favoured by whales,” he said from the Scottish island of Coll, where he was observing minke whales and dolphins last week. A marine mammal expert with the International Fund for Animal Welfare, Leaper has spent more than 20 years studying ship strikes and says that in Greek seas they account for more than 60% of whale deaths although most, he adds, go unreported and unrecorded.

Greece is not alone. The southern tip of Sri Lanka – one of the world’s busiest shipping routes – poses a similar danger for the blue whale population.

Environmentalists have won unexpected support from the shipping industry. The International Maritime Organization, acknowledging the problem, has drawn up guidelines.

Earlier this month, the International Whaling Commission urged the Greek government to take action, saying scientific evidence showed that ship strikes needed to be tackled.

“There are times when whales have been caught in the bow of a ship with half a tail ripped off,” Leaper says. “Sometimes you get a body that shows no external wounds but the bones have been crushed. In all cases it is a very horrible way to die.”

Prime minister Alexis Tsipras’s leftist-led coalition is expected to submit proposals to the IMO to reroute shipping lanes this summer. Frantzis and his team have helped identify waters that are prone to ship strikes because of the overlap of high densities of whales. Much of the research has been based on mathematical analysis conducted by Leaper, who believes shifting traffic five miles farther offshore would suffice. He also cites the example of approaches being altered to the Panama canal and off the coast of California.

“For a cruise liner going at 20 knots, that [five miles] would add 15 minutes to the entire journey,” he says. “It’s a pressing conservation and welfare problem and very easy to solve. Greece has the opportunity to come forward with proposals that will help resolve this, and might also help other countries come forward as well.”