The FDA won its two-year fight to shut down an Amish farmer who was selling fresh raw milk to eager consumers in the Washington, D.C., region after a judge this month banned Daniel Allgyer from selling his milk across state lines and he told his customers he would shut down his farm altogether.

The decision has enraged Mr. Allgyer’s supporters, some of whom have been buying from him for six years and say the government is interfering with their parental rights to feed their children.

But the Food and Drug Administration, which launched a full investigation complete with a 5 a.m. surprise inspection and a straw-purchase sting operation against Mr. Allgyer’s Rainbow Acres Farm, said unpasteurized milk is unsafe and it was exercising its due authority to stop sales of the milk from one state to another.

Adding to Mr. Allgyer’s troubles, Judge Lawrence F. Stengel said that if the farmer is found to violate the law again, he will have to pay the FDA’s costs for investigating and prosecuting him.

His customers are wary of talking publicly, fearing the FDA will come after them.

“I can’t believe in 2012 the federal government is raiding Amish farmers at gunpoint all over a basic human right to eat natural food,” said one of them, who asked not to be named but received weekly shipments of eggs, milk, honey and butter from Rainbow Acres, a farm near Lancaster, Pa. “In Maryland, they force taxpayers to pay for abortions, but God forbid we want the same milk our grandparents drank.”

The FDA, though, said the judge made the right call in halting Mr. Allgyer’s cross-border sales.

“Intrastate sale of raw milk is allowed in Pennsylvania, and Mr. Allgyer had previously received a warning letter advising him that interstate sale of raw milk for human consumption is illegal,” agency spokeswoman Siobhan DeLancey said.

Neither the FDA nor the Justice Department, which pursued the legal case, provided numbers to The Washington Times on the cost of the investigation and court fight.

Fans of fresh milk, which they also call raw milk, attribute all kinds of health benefits to it, including better teeth and stronger immune systems. Raw milk is particularly popular among parents who want it for their children.

In a unique twist, the movement unites people on the left and the right who argue that the federal government has no business controlling what people choose to consume.

In a rally last year, they drank fresh milk in a park across Constitution Avenue from the Senate.

But the FDA says it concluded, after extensive study along with the Centers for Disease Control and Prevention, that raw milk is never safer than pasteurized milk. It disputes those who say pasteurization — the process of heating food to kill harmful organisms — makes it less healthy.

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 FDA began looking into Mr. Allgyer’s operations in late 2009, when an investigator in the agency’s Baltimore office used aliases to sign up for a Yahoo user group made up of Rainbow Acres customers.

The investigator placed orders for fresh milk and had it delivered to private residences in Maryland, where it was picked up and documented as evidence in the case. By crossing state lines, the milk became part of interstate commerce and thus subject to the FDA’s ban.

At one point, FDA employees made a 5 a.m. visit to Mr. Allgyer’s farm. He turned them away, but not before they observed milk containers labeled for shipment to Maryland.

After the FDA first took action, Mr. Allgyer changed his business model. He arranged to sell shares in the cows to his customers, arguing that they owned the milk and he was only transferring it to them.

Judge Stengel called that deal “merely a subterfuge.”

“The practical result of the arrangement is that consumers pay money to Mr. Allgyer and receive raw milk,” the judge wrote in a 13-page opinion.

Grassfed On the Hill Buying Club has about 500 active members.

Liz Reitzig, a mother who has become a raw-milk activist and is an organizer of the group, said the lawyers who pursued the case against Mr. Allgyer ought to “be ashamed.”

“Many families are dependent on the milk for health reasons or nutritional needs, so a lot of people will be desperately trying to find another source now,” she said.

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