Mark H Durkan said he was "unconvinced of the advantages", and his decision would hold for the "foreseeable future".
The European Union said earlier this year that its 28 member states could adopt their own positions on the issue.
Each regional assembly within the UK is making its own decision.
While no GM crops are being grown commercially in the UK, imported GM commodities, especially soya, are being used mainly for animal feed, and to a lesser extent in some food products.
Mr Durkan said the relatively small size of farms in Northern Ireland could create "potential difficulties if we were to seek to keep GM and non-GM crops separate".
He said the costs of maintaining separateness could be expensive and impractical.
"Further, we are rightly proud of our natural environment and rich biodiversity," he said.
"We are perceived internationally to have a clean and green image. I am concerned that the growing of GM crops, which I acknowledge is controversial, could potentially damage that image."
The minister is responsible for all matters relating to the release of GM material into the environment, including the growth of GM crops.
Scotland banned GM crops in August.
Wales is maintaining what it describes as "a restrictive and precautionary approach to GM crop cultivation".
In England, the Department of Environment, Food and Rural Affairs has said it will only allow GM crops to be planted and the marketing of GM food or feed products if a "robust risk assessment indicates that it is safe for people and the environment".
It says each proposal would be looked at on a case-by-case basis, with an emphasis on the scientific evidence.
Eighteen million farmers in 28 countries grow GM crops on 181 million hectares, which is 13% of the world's arable land.
The main producers are the USA, Brazil and Argentina, and the leading GM crops are soya and maize.
Before GM crops can be grown in the EU, they have to be authorised. So far 48 genetically modified organisms have been licensed for potential use in animal feed in the EU.
Stormont's environment minister has banned the growing of genetically modified (GM) crops in Northern Ireland.