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WASHINGTON (AP)  The Agriculture Department ordered a biotechnology company Friday to pay more than $3 million in penalties for failing to prevent a genetically engineered corn that contained a vaccine from contaminating soybeans meant for human consumption.

The government stopped ProdiGene Inc.'s contaminated soybeans from entering the food supply, but the company has been ordered to pay about $250,000 in fines and nearly $3 million for the 500,000 bushels. That includes paying for destruction of the soybeans, said Agriculture Secretary Ann Veneman.

"It's the largest fine ever in a case like this," Veneman said.

It's the first time the agency has levied a fine against a biotechnology company for violating the Plant Protection Act, a law that regulates the transportation and planting of genetically engineered plants.

The company based in College Station, Texas, makes pharmaceutical and industrial enzymes and proteins by growing them in genetically modified corn. The government has strict guidelines for planting and removing such crops to make sure those products do not mix with the food supply or mingle with neighboring crops.

But ProdiGene failed to completely remove corn that contained a protein for a swine vaccine before planting soybeans in fields in Pocahontas County, Iowa, and Hamilton County, Neb. Inspectors discovered stray corn plants and ordered the company to remove them.

In the Iowa case, the company had to burn the corn. Inspectors found a similar situation in Nebraska, where the government ordered the contaminated soybeans to be impounded at a warehouse.

Anthony G. Laos, CEO and president of ProdiGene, said in a statement that the company wants to put the incidents behind it.

"We have learned some valuable lessons, and we hope the entire industry will benefit from our endeavors as we work with USDA on an enhanced compliance program," he said.

Bobby Acord, administrator of the Agriculture Department's Animal and Plant Health Inspection Service, said the company is working with the government to set up a more stringent training program to ensure a similar incident doesn't happen again.

Government officials also will increase inspections of ProdiGene's sites, he said.

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On the Net:

USDA's Animal and Plant Health Inspection Service: http://www.aphis.usda.gov