Authorities were investigating a new suspected case of crop contamination on Thursday – the second in the Pacific north-west in five months – after samples of hay tested positive for genetically modified traits.

The investigation was ordered after a farmer in Washington state reported that his alfalfa shipments had been rejected for export after testing positive for genetic modification. Results were expected as early as Friday.

If confirmed, it would be the second known case of GM contamination in a major American crop since May, when university scientists confirmed the presence of a banned GM wheat growing in a farmer's field in Oregon.

The suspected outbreak comes in the run-up to a ballot measure in Washington state that would require mandatory labelling of all GM foods.

Alfalfa is America's fourth largest crop, behind corn, wheat and soybeans, and the main feedstock for the dairy industry. A confirmed case of contamination could hurt the organic dairy industry, which is now worth $26bn a year, forcing farmers to find new sources of GM-free feed. It could also hurt a growing export industry. Alfalfa is increasingly sold for export but buyers, such as Japan, do not want GM products.

Campaigners said the suspected case of contamination provided further evidence of the difficulties of containing GM crops.

"It's telling that these things keep happening repeatedly," said George Kimbrell, senior attorney at the Center for Food and Safety in Portland, Oregon. "It's a systemic problem. We have a failed regulatory system for these crops."

The US Department of Agriculture (USDA) did not respond directly to questions about either GM incident. "USDA is working with Washington state to gather more information," a spokesman, Andre Bell said. He said the USDA was still investigating the GM contamination of wheat in Oregon.

The wheat variety was engineered by Monsanto, but the alfalfa farmer's seed was not. The company said in an email on Thursday it had no direct knowledge of the suspect contamination. But it also argued that existing regulations allowed for some GM impurities in conventional alfalfa seed. The spokesman, Thomas Helscher, further noted that GM was widely grown in America.

"Varietal purity standards followed by the alfalfa seed industry allow for low level presence of impurities, including GM traits, in conventional alfalfa seed," he said. "The potential presence of impurities is clearly stated on the label. If a grower is growing alfalfa for sensitive markets and wants specialized-GM free alfalfa, they can purchase non-detect alfalfa seed varieties, which is available from alfalfa seed suppliers."

The latest episode came to light in August, when a grower told the Washington state agricultural department some of his crop had been rejected for export after samples indicated the presence of GM material. The grower told officials he thought some of his seeds may have been mislabelled, according to Reuters, which broke the story.

GM alfalfa was the first engineered perennial crop approved by US regulators. It remains in the ground for three to six years and is widely pollinated by honey bees. Campaigners fought its introduction for a decade, arguing GM varieties were impossible to contain. They said escapes could damage conventional varieties. The crop was approved just two years ago.

In the case of the earlier contamination, GM wheat was never approved for human consumption. The crop had been raised on an experimental basis, and all samples were supposed to be have been quarantined or destroyed by 2005. The discovery of GM wheat on a farmer's field in eastern Oregon caused Japan and South Korea to temporarily halt some US wheat shipments.

In that instance, Monsanto spokesmen said repeatedly that the company believed the contamination was the result of sabotage.