These certifiers, then, are paid by the farmers and manufacturers they are inspecting to certify that the standards have been met. Depending on several factors, the fee can be hundreds or thousands of dollars. Manufacturers who buy six or seven organic ingredients to make one product are especially dependent on the web of agents.

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If agents do a thorough job, the system can be effective. But sometimes it falls apart.

Texas officials last month fired a state worker who served as a certifier because a plant owned by the Peanut Corporation of America — the company at the center of the salmonella outbreak — was allowed to keep its organic certification although it did not have a state health certificate.

A private certifier took nearly seven months to recommend that the U.S.D.A. revoke the organic certification of the peanut company’s Georgia plant, and then did so only after the company was in the thick of a massive food recall. So far, nearly 3,000 products have been recalled, including popular organic items from companies like Clif Bar and Cascadian Farm. Nine people have died and almost 700 have become ill.

The private certifier, the Organic Crop Improvement Association, sent a notice in July to the peanut company saying it was no longer complying with organic standards, said Jeff See, the association’s executive director. He would not say why his company wanted to pull the certification.

A second notice was sent in September, but it wasn’t until Feb. 4 that the certifier finally told the agriculture department that the company should lose its ability to use the organic label.

Mr. See said the peanut company initially appeared willing to clear up the problems. But he said the company was slow to produce information and then changed the person in charge of the organic certification, further delaying the process.