The government halted the research and ordered the destruction after discovering that a technician had sprayed a restricted pesticide on maize modified to resist attack by insects called stem borers.
Wilson Songa, Kenya's agriculture secretary and chair of the National Biosafety Committee, said this could compromise the validity of the trial's results.
On 25 August, the committee ordered the Kenya Plant Health Inspectorate Service to destroy the crops.
Songa was quoted in Kenya's Sunday Nation newspaper on 28 August as saying that local scientists had yielded to pressure from international organisations and were "rushing projects".
The maize was being grown in Kiboko by the Insect Resistance Maize for Africa (IRMA) project, a joint initiative of the Kenyan Agricultural Research Institute, the US-based Syngenta foundation, and the Mexico-based Center for Maize and Wheat Research.
In July, IRMA staff had notified the biosafety committee that the maize had been sprayed with the insecticide Furadan.
Stephen Mugo, IRMA's project coordinator, says the incident was unfortunate and a major setback to Kenyan research, but that GM maize field trials would continue.
"This is just like a battle we lost," said Mugo. "But the main war will continue until we help African maize farmers overcome the pest".
Stem borers destroy up to 12 per cent of maize growing in Kenya, amounting to US$76 million in lost harvests per year.
The IRMA project, which began six years ago, aims to develop both conventional and GM maize varieties to resist the pest.
The GM plants, which incorporate genetic material from a bacterium called Bacillus thuringiensis, have already been grown under experimental conditions in IRMA's US$12 million 'biosafety' greenhouse (