A frustrated fisherman has confessed that he stabbed to death dozens of protected sea turtles on a southern Japanese island after they got caught in his fishing nets, local officials say.

Between 30 to 50 green sea turtles were found dead or dying last Thursday, with stab wounds on their necks and elsewhere, on a beach in remote Kumejima island, some 1,600 kilometres (1,000 miles) southwest of Tokyo.

It was "an extremely grisly scene", according to Yoshimitsu Tsukakoshi, a senior staff member at Kumejima Umigame-kan, a local sea turtle conservation body. 

"Sea turtles are gentle creatures and they move away when humans approach them," Tsukakoshi told AFP on Tuesday.

"I couldn't believe it could happen in this day and age."

Yuji Tabata, the head of the local fishermen's cooperative, told AFP that the man responsible has confessed to stabbing the animals after dozens become tangled in his gillnet.

The fisherman, whose name has not been released, told the cooperative that he released many of the tangled-up turtles, but after struggling with the animals, he began stabbing them to try and weaken them.

"He said he has never seen so many turtles on his nets. He regrets it now," Tabata said.

"He said he felt in physical danger."

The local town government and police are investigating the deaths, a municipal official told AFP, declining to say whether the fisherman could face penalties over the incident.

An editorial in the local Okinawa Times newspaper on Tuesday condemned the deaths and the manner in which the protected animals were left to perish on the beach.

It also urged local officials to consider claims by fishermen that turtles are causing economic damage.

Local reports said some fishermen in the area believe the turtle population is increasing. 

The creatures can collide with fishing boats, injuring themselves and damaging the crafts' propellers.

Tabata said the community is also concerned that turtles are eating the seagrass that is home to the fish they depend on for their livelihood.

He stressed that the incident was rare and fishermen regularly untangle turtles caught in their lines.

"We are in the process of coming up with ideas so that this doesn't happen again," he added.