A yearlong sting operation, including aliases, a 5 a.m. surprise inspection and surreptitious purchases from an Amish farm in Pennsylvania, culminated in the federal government announcing this week that it has gone to court to stop Rainbow Acres Farm from selling its contraband to willing customers in the Washington area.

The product in question: unpasteurized milk.

It’s a battle that’s been going on behind the scenes for years, with natural foods advocates arguing that raw milk, as it’s also known, is healthier than the pasteurized product, while the Food and Drug Administration says raw milk can carry harmful bacteria such as salmonella, E. coli and listeria.

“It is the FDA’s position that raw milk should never be consumed,” said Tamara N. Ward, spokeswoman for the FDA, whose investigators have been looking into Rainbow Acres for months, and who finally last week filed a 10-page complaint in federal court in Pennsylvania seeking an order to stop the farm from shipping across state lines any more raw milk or dairy products made from it.

The farm’s owner, Dan Allgyer, didn’t respond to a message seeking comment, but his customers in the District of Columbia and Maryland were furious at what they said was government overreach.

“I look at this as the FDA is in cahoots with the large milk producers,” said Karin Edgett, a D.C. resident who buys directly from Rainbow Acres. “I don’t want the FDA and my tax dollars to go to shut down a farm that hasn’t had any complaints against it. They’re producing good food, and the consumers are extremely happy with it.”

The FDA’s actions stand in contrast to other areas where the Obama administration has said it will take a hands-off approach to violations of the law, including the use of medical marijuana in states that have approved it, and illegal-immigrant students and youths, whom the administration said recently will not be targets of their enforcement efforts.

Raw-milk devotees say pasteurization, the process of heating food to kill harmful organisms, eliminates good bacteria as well, and changes the taste and health benefits of the milk. Many raw-milk drinkers say they feel much healthier after changing over to it, and insist they should have the freedom of choice regarding their food.

One defense group says there are as many as 10 million raw-milk consumers in the country. Sales are perfectly legal in 10 states but illegal in 11 states and the District, with the other states having varying restrictions on purchase or consumption.

Many food safety researchers say pasteurization, which became widespread in the 1920s and 1930s, dramatically reduced instances of milk-transmitted diseases such as typhoid fever and diphtheria. The Centers for Disease Control and Prevention says there is no health benefit from raw milk that cannot be obtained from pasteurized milk.

Acting on those conclusions, the FDA uses its regulatory powers over food safety to ban interstate sales of raw milk and has warned several farms to change their practices.

According to the complaint the FDA filed in court, the agency began to look into Mr. Allgyer’s farm in late 2009, when an investigator in their Baltimore office used aliases to sign up for a Yahoo user group for Rainbow Acres‘ customers, and began to place orders under the assumed names for unpasteurized milk.

The orders were delivered to private residences in Maryland, where the investigator, whose name was not disclosed in the documents, would pick them up. By crossing state lines the milk became part of interstate commerce, thus subject to the FDA’s ban on interstate sales of raw milk. The court papers note that the jugs of milk were not labeled - another violation of FDA regulations.

Armed with that information, investigators visited the farm in February 2010, but Mr. Allgyer turned them away. They returned two months later with a warrant, U.S. marshals and a state police trooper, arriving at 5 a.m. for what Mr. Allgyer’s backers called a “raid,” but the FDA said was a lawful inspection.

The investigators said they saw coolers labeled with Maryland town names, and the coolers appeared to contain dairy products. The inspection led to an April 20, 2010, letter from FDA telling Mr. Allgyer to stop selling across state lines.

He instead formed a club and had customers sign an agreement stating they supported his operation, weren’t trying to entrap the owners, and that they would be shareholders in the farm’s produce, paying only for the farmer’s labor.

Customers hoped that would get around the FDA’s definition of “commerce,” putting the exchange outside of the federal government’s purview.

The FDA investigators continued to take shipments, though, and last week went to court to stop the operation.

Ms. Ward, the FDA spokeswoman, didn’t say exactly why they targeted Mr. Allgyer’s farm, but that violations generally are determined either by FDA investigations or by state-obtained evidence.

Pete Kennedy, president of the Farm-to-Consumer Legal Defense Fund, said undercover stings are not unheard of.

“It happens quite a bit. It’s almost like they treat raw milk as crack. It’s happened in a number of states, and at the federal level,” he said.

His organization has sued to try to halt FDA enforcement, and the case is pending in federal court in Iowa.

Mr. Allgyer’s customers declined to talk about the operations, and when asked whether they knew what would happen to the farm’s distribution, they said they would have to wait and see.

One of those customers, Liz Reitzig, president of the Maryland Independent Consumers and Farmers Association, said she started looking for raw milk when her oldest daughter began to show signs of not being able to tolerate pasteurized milk.

She first did what’s called cow sharing, which is when a group of people buy shares in owning a cow, and pay a farmer to board and milk the cow. But Maryland outlawed that practice and she was forced to look elsewhere for raw milk, and turned to Mr. Allgyer’s farm.

“We like the way they farm, we love their product, it’s super-high-quality, they’re wonderful. It’s just a wonderful arrangement,” she said.

“FDA really has no idea what they’re talking about when they’re talking about fresh milk. They have no concept - they really don’t understand what it’s like for people like me who have friends and family who can’t drink conventional milk,” Ms. Reitzig said.

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