Rural Affairs Minister Ross Finnie also insisted there was no risk to public health.
The "control" group at Daviot, in Aberdeenshire, has been found to have been planted with contaminated material from Advanta.
Advanta was recently at the centre of a row over the contamination of conventional seed.
The Scottish Executive said the latest discovery would have no impact on the final result of the trial.
Rural Affairs Minister Ross Finnie also insisted there was no risk to public health.
He stressed the trial oilseed rape would be destroyed upon completion of the research and would not be marketed. It would not enter the human or animal food chain.
Mr Finnie said he had consulted scientific advisers on whether action was needed.
"As a result of these extensive consultations, I am satisfied that the validity of the trial has not been compromised and our scientific advisers have confirmed there are no implications for the safety of the surrounding environment," he said.
"The strict conditions under which these trials are taking place mean that this site will be carefully and rigorously monitored."
He went on: "The contamination of the control crop with a GM variety does not affect the scientific merit of the trial.
'No change of plan'
"I must stress that the GM crop itself is not being assessed in these trials - it has been subjected to and passed numerous safety checks before it could be grown as part of the trial.
"The purpose of the farm trials is to assess the possible impact on the environment of growing a GM crop in commercial conditions and, in particular, using the herbicides necessary to give the GM plant its 'advantage'."
But the Scottish National Party called on the executive to end the GM venture.
Rural Affairs spokesman, Alasdair Morgan MSP, said: "This field trial has descended into a complete and utter farce.
"There is absolutely no point in proceeding with these tests now that it has been
revealed that both sets of oilseed rape planted on the farm are GM."
Scottish Green Party MSP, Robin Harper, said: "If the executive wants to get public opinion back on their side they
have no option but to order the pulling up of this crop.
"Failure to do so will simply confirm the public in their growing perception that this government and their Scottish Executive is still following a policy of cover up, delay secrecy and obfuscation in relation to GM."
The farmer conducting the Aberdeenshire trial said the revelations would not change her plans.
Shirley Harrison told BBC Scotland the level of contamination was so small, the trial would continue as agreed and would have no impact on the final results.
Information about the control plot contamination came to light after the executive sought further details on where the Advanta seed had been planted.