"Keep Out" reads a sign near the gated entrance at one site. Some of the stark, windowless warehouses require electronic pin codes and hazmat-style jumpsuits to enter. A sign on a metal gate ominously warns that it is a "Disease Control Area." Trespassers could bring a swift response from police geared up to fight bio-terrorism.

These aren't government labs, military facilities or weapons plants.

They are egg farms.

At clandestine farms across Pennsylvania, thousands of roosters and hens have been toiling away for months in confidential conditions normally reserved for important government ops. Their mission: Fertilize enough eggs to keep supplies of swine-flu vaccine flowing.

Fertilized chicken eggs are a central ingredient in the making of flu shots. They serve as miniature incubators that help the virus multiply before it is inactivated and turned into vaccine. As fears of a pandemic have grown in recent years, the U.S. government has helped finance the formation of extra chicken flocks to ensure enough eggs would be available for emergency vaccine production.

Sanofi-Aventis SA, a large vaccine maker, has been using as many as 600,000 eggs a day in its global swine-flu-vaccine production. GlaxoSmithKline PLC was using 800,000 a day at the peak of its production. Manufacturers get very few doses of swine-flu vaccine per egg -- from less than one to four.

In 2005, the U.S. classified these chicken barns as part of the nation's "critical infrastructure," giving them a kind of top-secret status. The secrecy is owing to worries that flu-related egg farms could be targeted for terrorist attacks or struck by chicken-killing pathogens.

The government wanted a "secure system to protect these birds," with "very strict conditions for the entry and exit of people and product," said Robin Robinson, an official at the Department of Health and Human Services who masterminded the secret egg program. "If we had no vaccine now it would be a very bad thing."

To ensure it had enough eggs to meet pandemic-level demand, the government invested more than $44 million in the program over five years; more than 35 farms are now involved in this feathered Manhattan Project.

No signs advertise the farms' involvement in the program, and visits from the outside world are discouraged. The government won't disclose where the farms are located, and the farmers are told to keep quiet about their work -- not even the neighbors are to know.

"If you were to drive through an agricultural area that had a lot of egg farms, I doubt that you could tell the difference between one of ours and one of anyone else's," said Rich Wisniewski, deputy director of purchasing services at Sanofi, which operates a large vaccine factory in northeast Pennsylvania.

"The difference is when you try to get access to those facilities," he said. Visitors must be accompanied by someone from Sanofi. Anyone entering the barns must wear a special hooded jumpsuit and step in a sanitizing foot bath, to ensure that diseases aren't passed to the birds. Trucks that deliver food and pick up eggs have to disinfect their wheels before entering the farms, which must be located within a day's drive of the vaccine factory.

The farms aren't guarded, but police keep watch over them, Mr. Robinson said.

"Do law enforcement at the local, state and federal level know they are there? Yes," he said in a phone interview, adding that police would quickly be on the scene if there was intelligence that said there was some kind of threat, including a "bio-terrorist-type threat." So far, no such incidents have occurred, he said.

Many aspects of the program are classified. The breed of hen? "That's proprietary," said Mr. Robinson. The rooster-to-hen ratio? "Proprietary." The number of eggs produced each year? Also proprietary. Mr. Robinson would say only that the egg suppliers are located in the "mid-Atlantic" region. He said some of the farmers are Amish.

Phone calls to egg farms in the mid-Atlantic region led to Pennsylvania Dutch Country, where many Amish people live. Farmers in the area identified several farms as suppliers for swine-flu vaccine, but the farms were quick to hang up when contacted.

"I'm sorry, we can't comment on that," said a man at one farm, declining to give his name. "Actually, we're not allowed -- we don't do interviews due to security reasons," said a woman at another farm, also declining to give her name.

A visit to one of the farms in Pennsylvania proved cryptic. A voice on an intercom at the main gate said the owner would come out to answer questions, but when a gray-haired man in a brown jacket appeared, he said little. He confirmed it was an egg farm but said he couldn't "confirm or deny" whether it supplied eggs for swine-flu vaccine. Asked about the obvious security measures, he said they were meant to keep the birds "free of disease." He declined to give his name.

Behind the gate, a semitruck was parked against one of the long barns. A fence surrounded the perimeter, with signs warning that it was "Private Property -- No Trespassing."

The eggs in the government program are produced under exacting guidelines. Mr. Robinson said the chickens are given special food made of corn or millet, with carefully controlled salt levels (too much salt can change the shape of the eggs or the number laid). The temperature and humidity in the barns are constantly monitored. And when the days grow shorter in the winter, the lights are left on longer, because light stimulates egg laying.

A hen typically lays an egg a day, whether it is fertilized or not. Eggs that are scrambled and eaten with toast are typically unfertilized. The kind used for vaccine need to be fertilized; vaccine makers inject flu viruses into the fluid surrounding the chicken embryo, where they multiply before being extracted, killed and blended into flu shots.

Secret government work appears to be a good deal for Pennsylvania's roosters. One rooster usually serves a harem of about 15 hens, keeping track of them in a crowd of thousands, said Gregory Martin, a poultry expert at Penn State Cooperative Extension, which provides educational programs for the agriculture industry. He said: "It's an open-floor system -- it's like the biggest dance floor you ever saw."

It's a different story for the hens. After nine months of service, they are typically euthanized because they can no longer lay "optimal eggs," Mr. Robinson said. "They've served their government," he said.

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