The compromise agreement was announced by Denmark, which holds the presidency of the EU.
The new rules have yet to be endorsed by the European Parliament.
The proposed rules will give the EU almost full legislation on the issue, opening the way to lifting a ban on GMO products imposed in 1999 by seven of the 15 member states.
Last month EU agriculture ministers agreed that food or animal feed containing more than 0.9% of genetically altered ingredients should be automatically labelled.
The agreed text foresees operators providing lists of 'all GMOs which have been used to make up the mixture'.
A revision clause was added to review the efficiency of the measure at the latest two years after the new regulations are implemented.
