Professor Anne Glover, herself a genetic engineer, is urging consumers to ignore labels like "Frankenstein foods" because they are misleading and damaging. The potential benefits of GM crops are "huge", she says, and the risks "extremely small".
But her enthusiasm for GM food has infuriated environmentalists, who fear she could exert an important influence on Scottish ministers. They argue that GM crops are "potentially dangerous" and point out that they have been widely rejected by the public and supermarkets.
Glover (50), a molecular biologist from the University of Aberdeen, was appointed chief scientific adviser earlier this year by the Deputy First Minister, Nicol Stephen. She is an expert on microbes and has genetically engineered bacteria to glow in the dark.
She has taken luminescence genes from deep sea organisms and transplanted them into soil bacteria. The healthier the soil, the brighter the bacteria glow, making it possible to use them as biological sensors for measuring environmental contamination.
It's that research - which has been commercialised - which informs Glover's view of GM foods. "I'm absolutely in favour of genetic manipulation carried out under appropriate guidelines," she told the Sunday Herald.
GM food could help end poverty and hunger in the world, as well as reducing farmers' use of hazardous pesticides, she said in an interview. "I think GM crops might well be able to help us in addressing some of these issues."
Crops could be engineered to resist drought, or to have a higher nutritional value, she argued. They could also be developed to produce high yields of biofuels to use as a renewable fuel for vehicles in place of oil.
Blight-resistant GM potatoes being trialed in England could help Scotland's potato market, she suggested. GM crops could also deliver cheaper foods with longer shelf lives.
"They have a significant amount to offer, globally, in terms of how they could be used to better produce crops under difficult conditions and to reduce the amount of chemicals used in agriculture," Glover stated.
The public debates that had so far taken place - including one inspired by the government - had been "really poorly informed", she claimed. "There's an astonishing lack of knowledge about genetic modification."
She didn't understand why people were prepared to eat fast food high in fat and preservatives known to be bad for health, but worried about GM. "The risks of GM foods is infinitely low compared to other things," she said.
Glover was particularly concerned about the widespread use of the term "Frankenstein foods" to describe GM products. "That's really unhelpful because you can do an enormous amount of damage by labelling something in that way," she said.
"We certainly need to learn from what's happened over GM foods to ensure that we don't allow developing new technologies with a huge amount to offer us to be hijacked by phrases which are all to do with headline-grabbing and nothing to do with reality."
But her views were fiercely rejected by the Soil Association, which promotes and certifies organic food. "There is no evidence whatever that Scottish consumers want GM products in their food supplies," said Hugh Raven, the association's director in Scotland.
"If the Scottish Executive's advisors can't grasp that in a democracy it's not very clever to foist potentially dangerous new technologies onto reluctant consumers, God help us all."
Raven pointed out that several studies had raised questions about the safety of GM organisms for human consumption. Some showed that modified genes could transfer into bacteria in the human gut.
Scottish ministers have postponed a long-promised consultation on the "coexistence" arrangements under which GM crops might be grown north of the border until next summer. No GM crops have been grown in Scotland since trials of GM oil seed rape ended in 2003.
The Scottish Greens' environment speaker, Mark Ruskell MSP, has proposed a bill to the Holyrood Parliament to make GM companies strictly liable for any economic damage caused by contamination from GM crop trials and commercialisation.
"I think the professor needs to wake up to the reality of GM crops and to the basics of plant biology. Once the GM genie is out the bottle, there is no going back," Ruskell said.
"She only needs to look to Canada where farming businesses have been left crippled after their crops have become contaminated. Given that GM crops would ruin the Scottish agriculture industry, I'm at a loss as to why the government's chief scientific adviser is determined to push this agenda."
Anne Glover, however, stressed that scientists should not impose GM onto an unwilling public. They should explain the benefits, leaving it up to people and politicians to decided what they wanted, she said. "I would like people to understand the technology and then make their own decisions.