Richard Lochhead said the Scottish government was not prepared to "gamble" with the future of the country's £14bn food and drink sector.
He is to request that Scotland be excluded from any European consents for the cultivation of GM crops.
But farming leaders said they were disappointed by the move.
Under EU rules, GM crops must be formally authorised before they can be cultivated.
An amendment came into force earlier this year which allows member states and devolved administrations to restrict or ban the cultivation of genetically modified organisms within their territory.
Mr Lochhead said Scotland's request for opt-outs from GM crop consent would cover an EU approved variety of genetically modified maize and six other GM crops that are awaiting authorisation.
He said that Scotland was known around the world for its "beautiful natural environment" and banning the growing of genetically modified crops would protect and further enhance its "clean, green status".
The announcement was welcomed by Scottish Green MSP Alison Johnstone, who agreed that the cultivation of GM crops would harm the country's environment and reputation for high quality food and drink.
But she called on ministers to go further by challenging big retailers to improve their labelling to show whether meat, eggs and dairy products come from animals fed on GM feed.
The move has also been broadly welcomed by environment groups.
