Greenpeace, pointing to independent laboratory testing, alleges that traces of a genetically engineered strain of rice known as " Liberty Link" had been found in beer made at the company's eastern coast US breweries in 2006.
Liberty Link is a series of strains of GM rice from Bayer CropScience.
Some of the strains are banned in a number of markets around the world for human consumption, but not in the US.
The claims could come as a blow for the global brewer, particularly in markets like the EU, where GM use continues to be met with opposition from both legislators and campaigners over claims that long-term impacts are not known.
However, Doug Muhleman, Anheuser Busch's vice president of brewing, operations and technology told BeverageDaily.com that the allegations were "false and defamatory" and that no contamination had been found by the brewer.
"All of our products are made according to the highest quality standards and in complete compliance with the laws in each country where we sell our beers," he stated.
Muhleman said that in the US the vast majority of commercial crops like corn contain genetically modified material approved as being safe for human consumption by the government.
He conceded therefore, that with the group using US long grain rice for all domestic beer production, there may be "micro levels" of Liberty Link strains in the product.
However, the GM strains are fully approved by the country's regulator for use in foods and drinks, he said.
Muhleman says that even in the chance that the GM rice may have been present during production, Liberty Link's proteins, like many other proteins, is significantly removed or destroyed by the brewing process.
"Liberty Link has not been found in any of our tests of our beers brewed in the United States," he stated.
Outside of its domestic operations though, GM use remains a contentious issue for food and beverage manufacturers, though Anheuser Busch claim it is confident that its international breweries were fully complaint with international laws.
"Neither [the company], nor our international licensed brewing partners use genetically modified ingredients, including genetically modified rice, in brewing products sold in any country with legal restrictions," Muhleman added.
The company said that it continually supports US farmers, resisting calls from Greenpeace to boycott GM crops.
The company alleges it is now facing retaliation for that stance from the environmental group.
However, Greenpeace claims that the Liberty Link rice was designated for test sites only and was never cultivated to be sold commercially.
The organisation added that the rice strain was still outlawed in most foreign markets despite being retroactively approved by the US Department of Agriculture.
Greenpeace said it was now calling on the brewer to commit itself globally to ensure all its beer ingredients were GM free, and to oppose the practice of growing rice products like Liberty Link in the US.
About 30 per cent of the 2006 US grain crop was contaminated by the LLRICE601 and LLRICE604 strains of genetically engineered Liberty Link rice, originating from Germany's Bayer CropScience.
The strains, which are linked to herbicide tolerance, both contain a protein called PAT, which according to the USDA has been safely used on other deregulated products for over a decade.
Though the exact details of how the contamination occurred were unknown, the resulting furore severely damaged the reputation of US rice, with 63 per cent of the year's total export trade of the product being disrupted, Greenpeace said.
Due to Anheuser Busch's position as the largest single purchaser of American rice, Greenpace claims that the group had a repsonsibility to ensure it was fully aware of how it is sourcing ingredients.
"Although Anheuser-Busch did not cause the genetic contamination of the rice, the company has a responsibility to their customers," the organisation stated.
"It should have refused to purchase or use any rice contaminated by the [GM] strains."