The decision to ban genetically modified crops in Scotland to “protect our clean and green brand” and avoid “gambling with the future of our £14 billion food and drink sector” was made without any prior consultation with the food industry, the Sunday Herald has learned.

A spokesman for Agriculture Secretary Richard Lochhead confirmed that the decision, which has already provoked widespread anger within the Scottish scientific community since it was announced earlier this month, was not based on input from Scotland Food & Drink, the public-private body established in 2007 to direct policy to enhance the Scottish food brand and boost exports.

Despite Lochhead’s claim, Scotland Food & Drink chief executive James Withers told this newspaper that GM was “not an issue” and “never part of the discussion” about the clean and green brand. He confirmed there had been no-consultation prior to the announcement.

Asked why industry views were not sought, the spokesman said the anti-GM stance “has been communicated by the Scottish Government for a number of years to the public and industry stakeholders”, implying that input from food producers themselves was superfluous.

One leader of a major Scottish food sector, who sits on the board of Scotland Food & Drink, told the Sunday Herald: “I’ve made a number of phone calls to colleagues in relevant industries and none of us was contacted in advance of this announcement. Why set up a body like this if you don’t bother to consult it?

“As a trade association we are happy to align ourselves to Government priorities but it has to be a two-way street. We certainly don’t expect to get our own way on every issue but we do expect to be consulted and listened to.”

As well as SFD, the Scottish Government is understood not to have explored the brand implications of GM with any other customer-facing food or retailing company or organisation, nor to have received representations from any food or drink producer on the desirability of a GM ban.

Lochhead did claim to “have heard directly from food and drink producers in other countries that are ditching GM because of a consumer backlash”, but his spokesman declined to provide details.

Under EU rules, GM crops must be formally authorised before they can be cultivated. Earlier this year an amendment came into force allowing member states and devolved administrations to restrict or ban the cultivation of genetically modified organisms within their territory. The Scottish Government is using the amendment to request Scotland be excluded from European consents for the cultivation of GM crops.

The backlash against the GM ban, which is supported by the Soil Association and the Scottish Greens, was expressed in a strongly-worded letter published last week, signed by 28 national and international scientific bodies and institutions, including the Roslin Institute, the Universities of Dundee and Edinburgh and the Royal Society of Edinburgh. In the letter to Lochhead, they voiced their “extreme concern” over the ban. They accused him of making a “political” gesture “not based on any informed scientific assessment of risk”, and betraying the Scottish Enlightenment-based tradition of evidenced research.

They wrote: “[GM] Traits currently being investigated that might benefit Scotland’s farmers, consumers and environment include potatoes that can reduce fungicide use and omega-3 enriched oilseeds that could provide a more sustainable source of feed for salmon farming. There are many other needs for the development of disease-resistant, pest-resistant and climate-resilient crops, where a GM method [could help]”.

Protests against the ban were also raised by the biologist Professor Dame Anne Glover, a former chief scientific adviser to the Scottish Government and to the EU, and by her successor in the latter role Professor Muffy Calder, who said she was “disappointed and angry” by the ban. She called on the Scottish Government to publish the scientific basis on which it was made. The spokesman declined to say whether or not it intended to comply.

Also expressing “disappointment” at the ban was the National Farmers' Union which said: “Decisions should be taken on the individual merits of each variety, based on science and determined by whether the variety will deliver overall benefit.”

In an article in The National last week, Professor Colin McInnes, James Watt chair of engineering at Glasgow University, argued for “open-sourcing” GM field trials in Scotland. “We could be leaders in the development of a global GM Wikipedia that puts new technology into public rather than private hands.”

He also quoted the 18th-century satirist Jonathan Swift: “Whosoever could make two ears of corn or two blades of grass to grow upon a spot of ground where only one grew before, would do more essential service to his country, than the whole race of politicians put together.”