In this Tuesday, Nov. 26, 2019 photo, Menhaden are stacked in a hold of the Windmill Point menhaden fishing boat at Omega Protein’s menhaden processing plant on Cockrell’s Creek in Reedville, Va. (Photo: AP)

NORFOLK, Va. (AP)- The Trump Administration is threatening to effectively ban a company that makes fish oil pills from fishing in the Chesapeake Bay over mounting concerns from regulators, governors and environmental groups about overfishing.

Earlier this year, the company Omega Protein exceeded harvest limits in the bay by more than 30% on a bony and oily fish called Atlantic menhaden.

The species is ground up and used in anything from health supplements rich with omega-3 fatty acids to high-end dog food. But the fish is also food for striped bass, humpback whales and other animals in the nation's largest estuary.

In a letter released Thursday, the U.S. Department of Commerce agreed with the Atlantic States Marine Fisheries Commission that the species is a vital link in the Chesapeake Bay's food chain.

The Commerce Department warned that Virginia lawmakers must bring the state into compliance with the commission's latest catch limits for the species. If they don't, the department said the state will face a moratorium in June.

Such a ban would primarily impact only one company, Omega Protein, although it would affect others that catch the fish in smaller amounts for bait.

Omega Protein has an operation based in Reedville, Virginia, that catches schools of Atlantic menhaden in the Chesapeake Bay as well as in the Atlantic Ocean.

The firm helps to anchor the economy in a rural stretch of Virginia along the bay's western shoreline. And it has enjoyed support from many of Virginia's lawmakers over the years, while contributing millions in political donations.

But in 2017, the interstate commission reduced bay harvest limits for Atlantic menhaden from about 87,000 metric tons to 51,000 metric tons.

Virginia’s legislature didn’t enact the change, and Omega Protein exceeded the cap this year.

The company and lawmakers who support it have said the catch limit is unfair and lacks scientific justification.

Omega Protein said Thursday that it would work with the commission and the state to abide by the latest harvest cap. But the firm also maintained its position that the limit isn't justified.

The company pointed to the commission's own coast-wide stock assessment for the species, which says that no overfishing is occurring.

“This is the first time that a moratorium has been placed on a fishery that is not overfished and is healthy by every measure,” the company said.

Max Appelman, a fishery management plan coordinator for the Atlantic States Marine Fisheries Commission, said the harvest cap is a precautionary measure based on recent fishery performance.

In February, the commission will review the findings of two benchmark assessments on the species, which could inform how Atlantic menhaden are managed along the coast and in the bay.

Omega Protein has increasingly drawn concerns from groups that include the Chesapeake Bay Foundation, The Nature Conservancy and the Virginia Saltwater Sportfishing Association.

Governors from nine Atlantic coast states, including Virginia Gov. Ralph Northam, recently voiced their concerns to the Commerce Department about protecting Atlantic menhaden.

Critics have also pointed out that the species is the most caught fish by volume on the Atlantic coast. And yet it also serves as food for young animals in the bay's protective waters.

“Menhaden are the lifeblood for predators from striped bass to dolphins to humpback whales to osprey, and they need effective conservation in their Chesapeake Bay nursery," said Joseph Gordon, project director for The Pew Charitable Trusts' initiative on conserving marine life in the U.S.