The vote this week was a "political blessing", an EU official told us.
It followed a European Parliament plenary vote on the 28 October.
Parliament voted in the draft regulation 359 to 202 votes with 127 abstentions, however two parts of the compromise deal were rejected during the vote relating to the wording of article 9.3 and recital 27 on the uniform updating of the EU's novel food list.
This latest Council vote ousts these uncertainties and sees the regulation pass into the final stage before being written into law.
The EU official said these "meaningless" rejected points were a simple question of wording and did not change the substance of the regulation.
The Council will formally adopt the new regulation on 16 November before it is published in the Official Journal of the EU. It is unlikely there will be any changes at this stage.
It comes into force 20 days after publication and will be applicable two years later.
Lydia Mutsch, member of the Luxembourg government and president of the Council, said in a release on Wednesday: "The compromise approved today is a needed step towards faster innovation in the novel foods market while guaranteeing high levels of consumer protection for the European citizens."
Quicker and cheaper
Under the new centralised system whereby applications pass through the European Food Safety Authority (EFSA) not member states, the authorisation procedure is expected to take around 18 months compared to three years under the previous rules.
It will also account for generic authorisations – meaning once a food or ingredient is approved it will be approved for any business to use.
Friendly neighbour
The rules also open up approval to foods consumed traditionally outside of the EU.
Companies must prove these foods have been safety consumed by a significant part of that non-EU country’s population for at least 25 years.
EFSA will now decide the level of evidence needed for such applications.
Little big issues
The regulation explicitly covers nanotechnology, however it is up to the European Commission now to adapt the definition of engineered nanomaterials to meet technical progress or the definitions agreed at international level.
Insects will also be covered under the regulation, confirming that insects must seek authorisation before going to market.
Spot the difference
While food from animal clones remain within the scope of the new novel food rules, the Council and the European Parliament are currently discussing specific rules for this controversial subcategory.