At least five whales have died after nine beached themselves off Italy's southern coast, in what experts called a highly unusual event in Mediterranean waters.

The whales, measuring up to 10 metres long and weighing several tonnes each, were found stranded off the coast of Puglia on Thursday, the environment ministry said. Four were already dead and the rest were dying, the ministry said.

Nine whales initially beached themselves but two managed to escape into deeper waters, environmental group Greenpeace said, calling it "extraordinary" both for the size of the beaching as well as the unlikely presence of whales in the area at this time of the year.

Another whale died today and the remaining two will be put down since there is little hope of saving them, local news agencies reported.

"A massive beaching is extremely rare in the Mediterranean," biologist Maurizio Wurtz at the University of Genoa told La Stampa daily. Experts say the beachings are more likely to occur in areas like Australia.

Conservationists and biologists said pollution or noise from naval activities or petroleum surveys could have confused whales and interfered with their communication and led to the incident.

Italy's coast guard said an operation was underway to recover the carcasses so that autopsies could be conducted.