The new law only applies to crops and does not cover GM used in animal feed, which can still enter the human food chain indirectly.
Although Euro MPs and ministers have agreed to give states more flexibility, EU scientists will still play a key role in authorisations.
A type of maize - MON 810 - is the only GM crop grown commercially in the EU.
Spain is by far the biggest grower of MON 810 in Europe, with 137,000 hectares (338,000 acres)
MON 810 is marketed by US biotech giant Monsanto and is modified to be resistant to the European corn borer, a damaging insect pest.
The maize variety is banned in Austria, Bulgaria, France, Germany, Greece, Hungary and Luxembourg.
GM crops are used widely in the US and Asia, but many Europeans are wary of their impact on health and wildlife.
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