Officials are investigating claims unlicensed strains of oilseed rape were cultivated at sites near Lincoln and Market Rasen.
Experts think the seed varieties may have got into the tests sites during production.
Ministers are investigating the incident and say the may prosecute Aventis CropScience, which supplied the seeds.
Regulations breached
The mistake was uncovered by routine monitoring of genetically-modified crop trials in Lincolnshire.
The contamination involving Aventis oilseed rape breaches the regulations governing GM crops.
The Department for Environment, Food and Rural Affairs (Defra) says the contamination has been found at two sites at Boothby Graffoe between Lincoln and Grantham and at two other areas at Thorganby and Ludford - both near Market Rasen.
It is understood the mix-up happened because seeds that were supposed to be used in the trials got mixed up with other strains not licensed for release during the production process.
All the crops involved are due to be harvested and destroyed and the government says there is no risk to health or the environment.
Aventis says GM oilseed rape varieties have been grown in trials in the UK since 1989 and commercially in Canada since 1995 on many millions of acres, without one reported detrimental incident regarding human and animal health or the environment.