But scientists behind the British study also stressed that the differences between the two arose not because the crop was genetically engineered but because of the way pesticides were applied.
"The study demonstrates the importance of the effects of herbicide management on wildlife in fields and adjacent areas," researcher David Bohan said.
Green groups, however, were aghast. "These results are yet another major blow to the biotech industry. Growing GM winter oilseed rape would have a negative impact on farmland wildlife," Friends of the Earth campaigner Clare Oxborrow said.
The study was the last in a four-part $9.5 million test of controversial technology - the largest experiment of its kind in the world.
Scientists said that when compared with conventional winter-sown rapeseed, GMO herbicide-resistant plants kept the same number of weeds overall, having more grass weeds but fewer broad-leaved weeds.
"The study demonstrates the importance of the effects of herbicide management on wildlife in fields and adjacent areas"
Flowers of broad-leaved weeds provide food for insects, while their seeds are an important food source for other wildlife.
Researchers said that while fields planted with the biotech version were found to have fewer butterflies and bees, differences arose not because the crop was genetically-changed but because of the way they were sprayed.
In October 2003, the same government trials found that GMO sugar beet spraying was significantly more damaging to the environment than the management of conventional varieties.
They also concluded that gene-spliced spring-sown rapeseed may also have a negative impact on wildlife, while GMO feed maize did not.
The biotech lobby insists the crops are safe.
"GM crops offer a better, more flexible weed management option for farmers and, as the results today indicate, the difference between the impact of growing GM and non-GM crops on biodiversity is minimal," Tony Combes, deputy chairman of the Agricultural Biotechnology Council, which represents biotech firms like Monsanto and Syngenta, said.