A company that holds a lease to harvest shellfish in more than 1,800 acres of Oyster Bay and Cold Spring Harbor has all required federal permits, the U.S. Army Corps of Engineers recently determined after representatives of independent harvesters filed complaints alleging violations of federal law.

The determination is the latest chapter in a decades-long battle between independent harvesters and Frank M. Flower & Sons, which has a 30-year lease with the Town of Oyster Bay through 2024.

The baymen have accused Flower of destroying the bay bottom and harming marine life with its mechanical dredging. Flower denies the charge and says it is in the company’s interest to keep the bay healthy. Most Flower operations occur within the Oyster Bay National Wildlife Refuge.

The Army Corps investigated complaints from several baymen and determined that Flower is in full compliance with what the Corps calls a “nationwide permit” for shellfish harvesting, agency spokesman Hector Mosley said.

Flower attorney James Cammarata said the company is “properly permitted and we’re properly authorized to do what we do. And everything we do is safe and does not disturb the environment.”

Robert Wemyss, secretary of the North Shore Baymen’s Association, who had urged the Corps to shut down the Flower operations, alleged the Corps and the New York departments of State and Environmental Conservation allowed Flower to flout federal and state law for years.

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“They’re completely ignoring the regulations,” Wemyss said.

A Department of State spokesman said Flower currently needs no permit from the agency. DEC officials said Flower has all required permits.

William Painter, president of the North Oyster Bay Baymen’s Association, said that “if the state and feds would do what is required and perform a necessary study,” they would confirm the harm dredging is doing to the bay.

“That dredging is an environmental disaster,” he said.

There have been multiple calls for an independent study of the dredging, but no agreement on who would conduct and pay for it.

The DEC said shellfish harvest data “does not suggest a decline in Oyster Bay’s shellfish population.”

A 2011 National Oceanic and Atmospheric Administration report concluded that effects of dredging near shorelines “are generally short-lived” and “minor” compared with natural disturbances such as storms.

But NOAA officials said the impact varies depending on the location and the equipment used. Christopher Gobler a professor of coastal ecology and conservation at Stony Brook University, said frequency of operations is also key. If a section of bay bottom is dredged often enough, especially during summer spawning season, “that doesn’t give the bottom a chance to sort of reset and re-establish itself.”

Dredging muddy bottoms also can release sulfide and nitrogen, which at high enough levels can be toxic to marine life, Gobler said. He also called for a thorough study of Oyster Bay.

“To be certain you need data,” he said. “Without that, you’re relying on speculation.”