The instruction by Archer Daniels Midland (ADM), based in the farming heartland of Illinois, was made after food producers using the company's raw soya flour and oils threatened to take their business to suppliers that could guarantee GM-free soya.
The effect could be to discourage farmers from buying GM seeds. It also casts doubt on a claim repeatedly made by the farmers since GM soya was introduced in 1996 - that it would be too difficult to separate the GM and conventional strains after harvest.
ADM, which has revenues of $14.2bn (pounds 9bn), told farmers the move was in response to food manufacturers that are "requesting and making purchases based on the genetic origin of the crops".
Some operators of the grain "elevators", which prepare the crop for processing, said that segregation could significantly slow this year's harvest.
In the UK, Sue Davis of the Consumers' Association said: "We have always called for segregation of GM and conventional crops. Now it seems like we are moving towards consumers getting choice on GM foods. It also shows that consumer concern about GM is having an impact all the way through the food chain."
The use of soya, which appears in about 40 per cent of processed foods, has led to growing consumer protest in the UK over the lack of labelling of GM soya. About 40 per cent of the US soya harvest will be GM this year. In the UK, supermarkets have vied to eliminate GM soya from their products, and to label brands containing it.
Earlier this year, ADM told farmers it would no longer accept GM crops that are not approved for import in Europe, even if they can be grown in the US.Reuse content