A worker places wheels of cheese on a wooden racks in a cooler at Vella Cheese on June 10 in Sonoma, California. (Justin Sullivan/Getty Images)

Is the Food and Drug Administration waging a war on artisanal cheese?

The answer depends on your perspective. But this much is certain: An FDA official’s remarks to New York regulators about using wooden boards to age cheese has caused an uproar in the domestic industry and raised questions about the status of imported cheeses that use the same process.

The flap dates to 2012, when an FDA inspection of a small cheesemaker in upstate New York found the presence of Listeria monocytogenes, a potentially harmful bacterium, on a board used to age the company’s Gouda-style cheese. When inspectors found evidence of listeria again in 2013, the agency ordered the company to halt its sales until it developed a listeria-control program.

The Department of Agriculture and Markets in New York, which like other states has long allowed the use of wooden boards to age cheese, sought clarity from the FDA on the technique, which has been used for hundreds of years in the United States and Europe.

In a response early this year, Monica Metz, chief of the dairy and egg branch at the FDA’s Office of Food Safety and Applied Nutrition, wrote that using wooden boards for aging cheese doesn’t conform to established good manufacturing standards because the boards cannot be “adequately cleaned and sanitized.”

Wheels of jack cheese age on wooden racks in a cooler. (Justin Sullivan/Getty Images)

“The porous structure of wood enables it to absorb and retain bacteria, therefore bacteria generally colonize not only the surface but also the inside layers of wood,” Metz wrote. Because the wood boards touch the final food product, she noted, “They could be a potential source of pathogenic microorganisms in the finished products.”

Over the weekend, Cheese Underground, a popular blog run by self-proclaimed cheese geek Jeanne Carpenter, detailed the growing angst among artisan cheesemakers over the FDA’s assertion. “A sense of disbelief and distress is quickly rippling through the U.S. artisan cheese community,” she wrote.

It didn’t take long for apocalyptic headlines and attacks on the “nanny state” to pop up on the Internet.

“FDA May Destroy American Artisan Cheese Industry,” warned Forbes. “FDA Rules Against Centuries Old Cheese-Making Process,” said the Daily Caller. “The FDA’s Misguided War on Bacteria That Makes Cheese Taste Good,” said a Slate column.

The FDA tried to clarify its position Tuesday, saying that Metz’s reply was merely a response to questions, not a statement of policy. The agency said in a statement that it has no new policy in place and has never taken an enforcement action “based solely on the use of wooden shelves.”

Late Wednesday, the FDA released another update, reassuring cheesemakers that the agency has little interest in cracking down on the age-old use of wooden boards and calling reports to the contrary inaccurate.

“To be clear, we have not and are not prohibiting or banning the long-standing practice of using wood shelving in artisanal cheese,” the FDA said in the statement, acknowledging that the language used in its correspondence with New York regulators “may have appeared more definitive than it should have, in light of the agency’s actual practices on this issue.”

The FDA’s initial explanation offered little clarity — and apparently little comfort — to specialty cheesemakers from New York to Wisconsin to California, who worried that their livelihoods may be upended over something they say has never caused a problem.

“Eighty-five percent of my business revolves around aging cheese on wood,” said Chris Roelli, a fourth-generation cheesemaker in Wisconsin. “This could be potentially devastating.”

Roelli said the wood he uses for his cheddar blue cheese helps provide a distinct flavor while controlling moisture and allowing the rind to develop properly.

He and other cheesemakers pointed to scientific studies that have concluded that wooden boards are safe. Just last year, researchers at the Wisconsin Center for Dairy Research found that “the use of wood boards does not seem to present any danger of contamination by pathogenic bacteria as long as a thorough cleaning procedure is followed.”

This isn’t the first time the FDA has tangled with the upscale cheese community. The agency struck a nerve last year when it began blocking imports of Mimolette, a Gouda-like cheese from France with a small but fervent following in the United States.

For centuries, microscopic mites have been part of the process of making the cannonball-shaped, electric-orange cheese. But last spring, FDA inspectors began halting shipments at the border, stranding thousands of pounds in warehouses. Inspectors said they found too many cheese mites per square inch on Mimolette’s cantaloupe-like rinds.

Cheese lovers denounced the blockade. Although the FDA never explicitly banned Mimolette, imports have all but dried up.

“It is completely stopped,” said Benoit de Vitton, North American representative for Isigny Sainte-Mère, a top Normandy-based exporter of Mimolette. “We are only selling the young version of it, aged only three months and waxed so the cheese mites can not go inside the rind. It is a good cheese, but does not have the flavors developed during the long months of ripening on wooden boards.”

The confusion about how forcefully the FDA intends to pursue the wooden-boards issue has left many artisan cheesemakers in limbo, said Robert Ralyea, a senior extension associate at Cornell University who made the original inquiry about wooden boards to state regulators.

He said producers face a quandary if state inspectors allow the boards and the FDA does not. “It’s hard to keep two regulatory agencies happy,” he said.

Meanwhile, a bipartisan group of lawmakers on Capitol Hill led by Rep. Peter Welch (D-Vt.) have said they will try to block the FDA from interfering with the wood-aging process if the agency doesn’t work with cheesemakers to find a solution.

Roelli, the Wisconsin cheesemaker, said his family’s small business might be jeopardized if cheesemakers and the FDA cannot come to a compromise on the issue.

“Everything we’re doing right now would have to change. If I’m not able to do that, I have to find a new way to survive,” he said. “I don’t have a Plan B.”