As two tractors hauled the 60-foot-long carcass of a finback whale that was the center of attention in Southampton last week the Shinnecock Indians got a piece of bad news: They would not be getting to keep the fins and tail flukes from the whale as they had requested.

Federal law forbids anyone from taking parts of federally protected whales without permission from the National Oceanographic and Atmospheric Administration, which can take up to two weeks. The scientists, who had been authorized to hold the fins until that approval could be secured, said they could not preserve them for that long.

The Shinnecocks pointed to a pre-colonial agreement with the founders of Southampton Town that gave them the rights to any whales that wash ashore, once a more common occurrence, but were rebuffed by federal officials who said they would have to go through the same approval channels as anyone else.

The tribe will get to keep the long strands of baleen from the mouth of the whale to display in their tribal museum, but the loss of the fins was a disappointment to members of the tribe that has been credited by some as having been pioneers in the hunting and use of whales—and possibly the founders of the once great whaling industry in America.

This appearance of this week's behemoth and the clash with the Shinnecocks, spotlighted the long history of whaling on the South Shore and by the tribe.

The tribe once saw the stranding of a whale as a gift from the sea, one tribal leader said this week, and the tribe's members traditionally used the fins and tail flukes of whales in religious ceremonies to give thanks for the bounty of food and bones. But few, if any, living members of the tribe have gotten to participate in such a ceremony because last week was the first time a whale had washed ashore in Southampton Village in more than 40 years. The tribe had hoped to rekindle its tradition with this whale's flukes.

"It is something most of our members have never experienced," Tribal Trustee Charlie Smith said last week. "It's part of our history and a tradition that we need to carry on for our young members."

For centuries, the Shinnecock and Montaukett tribes were among a handful of Native American tribes that actively hunted whales. Some historians have credited the Shinnecocks with having taught the practice to white settlers who eventually founded what would become a mammoth industry based on hunting whales along the East Coast of America and eventually across the seven seas.

In ancient times, the Shinnecocks pursued whales in dugout canoes. As many as 20 canoes carrying up to 100 men would hunt a single whale. With harpoons and spears fashioned out of sharpened deer antlers and the bones of other whales, they dispatched the giant sea creatures by stabbing at them and then following the whales until they bled to death and could be towed ashore. According to a book on the history of East End whaling by Sag Harbor attorney Paul Bailey, the Shinnecocks would sometimes simply herd whales into the shallows where they could be killed by others wading in the surf.

Writings and historical accounts that detail this practice among the Shinnecocks and other Northeastern tribes are unclear about the extent to which the whales were relied on as a food source but often refer to the skill at the hunt displayed by the Shinnecocks in particular. The Shinnecocks are known to have used various parts of whales for tools and decorations and possibly as a food staple, but not to an extent that would be require large numbers of kills.

That, of course, would all change when white settlers arrived in the new world. Soon whales were highly sought after for their blubber as oil, sperm and bone, and shore-based hunts became common. The Shinnecocks were soon sought after for their honed skills at pursuing and killing the whales and made up the bulk of crews that manned the shore launched whaling skiffs that replaced canoes in colonial times. When large ocean-going ships began wandering the world in search of whales, Shinnecocks were at the heart of the crews they carried with them as well.

According to Southampton Historical Museum director Richard Barons, records at the Nantucket Whaling Museum indicate that a white man from eastern Long Island, who said he had learned how to hunt the whales from natives there, brought the skills he had learned to settlers, kicking off the growth of one the world's largest and most famed whaling ports.

"They may have been the ones that birthed the entire whaling industry," Mr. Barons said. "We know they were doing it well before anyone else and some of the first white whalers came from this area, so it stands to reason."