The beaching of 46 pilot whales on a small island in south-eastern Indonesia – during which all but three died – has turned into an unexpected mealtime bonanza for locals, who have taken the meat for food, a common practice for the region's whale hunters.

Many of the whales were already dead when they were discovered by locals on Sabu island's Raijua beach in East Nusa Tenggara province on Monday. According to island official Marthen Dira Tome, some had become injured after being battered against the surrounding coral reefs.

"Six of the whales were exhausted so they were dragged back to shore. Most probably, they would not have been able to swim due to their injuries," Tome told the Jakarta Post.

Some locals and animal activists struggled to help send the few surviving whales out to sea, as they repeatedly swam back to shore.

According to Pramudya Harzani of the charity Jakarta Animal Aid Network, which was on hand to help rescue the whales, the beaching may have been partially due to the rapidly receding tides of the seasonal monsoon. But scientists believe pilot whales follow a group leader to shore when one becomes sick, stranding them all together.

Locals around Sabu island are known for their traditional whale-hunting methods, particularly those from Lamalera village on neighbouring Lembata island. Fishermen in rowboats use hand-made harpoons to hunt sperm whales in the same way they have for centuries, later trading what they don't eat or use from the carcass with other islanders.

Because of their traditional practices, whale hunters are exempt from the UN's international ban on commercial whaling, but in recent years the village has come under pressure from local charities and the Indonesian government to help create a protected maritime zone in the area.