The US biotech industry said it was "not surprised" by the findings because many farmers are unwittingly planting billions of GM seeds a year.
By spreading genetic modification throughout US agriculture, the report concludes there are increased dangers to health.
For example, the next generation of GM crops are bred to produce pharmaceuticals and industrial chemicals - a development that could lead to drug-laced cornflakes for breakfast.
Under the auspices of the Union of Concerned Scientists, two separate independent laboratories tested supposedly non-GM seeds.
The seeds represented "a substantial proportion of the traditional seed supply" for maize, soya and oilseed rape, the three crops whose modified equivalents are grown widely in the United States.
The test found that at "the most conservative expression", half the maize and soyabeans and 83% of the oilseed rape were contaminated with GM genes.
"Heedlessly allowing the contamination of traditional plant varieties with genetically engineered sequences amounts to a huge wager on our ability to understand a complicated technology that manipulates life at the most elemental level"
Union of Concerned Scientist's report
The surprise results come just eight years after the modified varieties were first cultivated on a large scale in the US.
The degree of contamination was previously thought to be at a relatively low level of about 0.5 to 1%.
But the US report says that "contamination ... is endemic to the system".
"Heedlessly allowing the contamination of traditional plant varieties with genetically engineered sequences amounts to a huge wager on our ability to understand a complicated technology that manipulates life at the most elemental level."
There could be "serious risks to health" if drugs and industrial chemicals from the next generation of GM crops got into food.
Lisa Dry, of the US Biotechnology Industry Association, said the industry was "not surprised by this report, knowing that pollen travels and commodity grains might co-mingle at various places".