Something’s getting stinky in Washington, where lawmakers are rushing to protect American-caught catfish from stiff new inspections they themselves set up just a few years ago.

It’s the latest flare-up in a decadelong feud that saw Congress insist on setting up a special inspection system for catfish, hoping to chase foreign imports out of the U.S. market — only to now balk when the same inspections are set to hit U.S.-caught fish.

Florida’s two senators wrote a letter this week asking that the American wild-caught catfish industry be exempt from the inspections, while Maryland’s governor earlier this month asked for an exemption for that state’s blue catfish in the Chesapeake watershed.

They’re rushing ahead of a Sept. 1 deadline, when the Department of Agriculture’s Food Safety and Inspection Service (FSIS) is slated to take over catfish inspections from the Food and Drug Administration under a law passed by Congress in 2008 and reaffirmed in 2014.

Watchdog groups say it’s an example of government run amok, wasting millions of dollars a year on duplicative inspections — all to protect the catfish industry in states along the Gulf of Mexico, who fear cheaper competition from Vietnam and China.

“[It’s] quintessential pork-barrel politics,” said David Williams, president of the Taxpayers Protection Alliance. “This is something that should not be around one day longer.”

Most fish are inspected by the FDA. But Congress, led by Sen. Thad Cochran, a Mississippi Republican looking to protect his state’s industry, decided catfish needed a more intrusive inspection, so it demanded the Food Safety and Inspection Service — a branch of the USDA — get involved.

Over the last year and a half, the FSIS has been ramping up and, as of the beginning of this month, was inspecting imports.

Sean Bergen says his Maine-based company, Sustainable Seafood Sales LLC, had imported about 50 shipments over the past 18 months, under FDA inspection, with little problem.

But his latest shipment this month ran into problems now that the Department of Agriculture is in charge. He said he brought in a small shipment to Miami, but the USDA inspectors held it up. Ultimately they decided it was safe for consumption — after it had expired and needed to be destroyed.

Mr. Bergen said the FSIS’ errors are costing him.

“They are learning on my dime,” Mr. Bergen said.

Powerful lawmakers, however, back the USDA inspections, saying they are more thorough than what the FDA has done. They say the new inspections help prevent fish tainted with illegal disinfectants and other drugs from reaching dinner tables in the U.S.

In the first two weeks of the transition period, the USDA blocked more tainted catfish from entering the U.S. market than the FDA had blocked in the previous two years, said Sen. Roger F. Wicker, Mississippi Republican.

“Now that the USDA has completed the transition and is inspecting 100 percent of catfish imports, American consumers can expect a much higher level of food safety from catfish purchased in the United States,” Mr. Wicker said.

“Moreover, our domestic producers are now competing on a level playing field with foreign producers, and can be assured that their wholesome, quality-controlled catfish will not be undercut or devalued by substandard foreign fish flooding the U.S. market,” he said.

Mr. Wicker and Mr. Cochran have been two of the most prominent champions of the new system.

Mr. Cochran is chairman of the Senate Appropriations Committee, and the 2017 spending bill reflected his stance: It included a statement praising the “diligent work” of the FSIS, crediting the new inspections for preventing more than 273 tons of “adulterated or ineligible” fish from entering U.S. commerce since early 2016, when the transition from USDA to FSIS began.

It’s unclear how dangerous the catfish were, though. The Government Accountability Office has repeatedly said the old system, with the FDA inspecting catfish, was working fine, and also cited FDA officials describing catfish as a “low-risk product” in a 2012 report.

The GAO said the USDA inspections would cost $14 million a year for the duplicative inspectors, though the latest figures from FSIS lower the cost estimate to $2.6 million a year.

Important lawmakers whose states are about to get snared by the stiffer inspections are now asking for relief.

Sens. Marco Rubio and Bill Nelson of Florida asked Agriculture Secretary Sonny Perdue this week to exempt domestic, wild-caught catfish from new enforcement rules.

“Seafood processors and commercial fishermen in Florida and around the country do not need the additional burden of a duplicative inspection process,” the senators wrote.

Maryland Gov. Larry Hogan raised similar issues in a letter to Mr. Perdue earlier this month, saying the more intrusive checks will disrupt an emerging blue catfish market in his state that’s simultaneously helping lower the population of the “invasive” species.

He said the state’s efforts to promote eating nonnative blue catfish from the Chesapeake Bay watershed have created jobs and supplied millions of pounds of catfish to consumers in the Washington, D.C., area.

“Unfortunately, the expense and regulatory hurdles associated with the new USDA catfish inspections put this new industry and the fishermen who depend on it in jeopardy and will reverse the [progress] we have made,” Mr. Hogan wrote.

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