The almost unanimous 'yes' vote (614 for, eight against) came as no surprise as most of the political parties reached an agreement on the compromise.
The main point of the regulation is that the European Commission will draw up a positive list of well-established claims, such as "calcium is good for your bones". The positive list will be drawn up within three years, based on submissions from member states.
Any claims submitted for the list after this period, or any disease reduction claims (such as "X helps reduce the risk of osteoporosis" will have to be assessed by EFSA and approved by the Commission.
The main stickling points however, were in the details and procedure, such as whether to impose a full authorisation or a notification procedure for the entry of products bearing health claims to market.
The Council was in favour of the former, and the Parliament the latter, which would allow the company to make the claims unless objections were raised or evidence requested. This, it was envisaged, would speed up the time to market and compliance would also be less expensive for food companies, and therefore not be such as barrier to innovation.
The compromise reached last week established a registration mechanism that falls between the two. It sets a maximum time frame for assessment by the European Food Standards Agency (EFSA) to review registration dossiers, possibly of eight months, whereas under the authorisation model no time frame was given.
Another was over article four, on nutrient profiling. Under the original proposal foods with a high content of substances regarded as detrimental to health, such as sugar or fat would be barred from carrying health claims even if they were also rich in or fortified with other beneficial nutrients.
Under the compromise package, foods that do not respect the nutrient profiling would still be able to make health claims as long as only one nutrient exceeds the limit and this is indicated on the label.
Trademarks are also to be included in the regulation. The Parliament had wanted trademarks to be excluded, since many companies have spent years and much resources on building recognition, and it would be confusing for consumers who already recognise the health associations if they were suddenly pulled of the shelf.
However the agreement grants trademarks that were already on the market before January 2005 a 15-year window to comply.
David Hare, consultant at health and diet lobbyist The Whitehouse Consultancy, called this "fudge", and said it is not clear when a trademark constitutes a health claim and when it does not.
"This will have to be sorted out in guidance to be applied by individual food standards agencies," he told NutraIngredients.com.
Individual doctors and healthcare professionals will not be able to endorse products for their health benefits, but endorsement by health charities and other organisations may be permitted under national rules.
"Charities still need to look out, as endorsements are an important revenue source for them," said Hare.
EFSA commissioner Markos Kyprianou said after the vote: "Like any compromise, each side would have liked to go further, but this is a good compromise which takes account of all positions in a balanced way."
The next step is for the Council of Ministers to debate the regulation in June, and vote in September, Hare told NutraIngredients.com. The regulation could then come into force before the year is out and be applied six month afterwards, from around April 2007.
But there is still a chance, however small, that a spanner could be thrown in the works if one of the major political European nations like France or Germany votes against it at Council.
Miguel Fernandes da Silva, adviser for European Advisory Services said that neither the Socialists nor the Christian-Democrats were happy with the result.
After calling the package "as awful as the original Commission proposal," Ms Renate Sommer, shadow rapporteur from the EPP group, signaled that she would ask the German government to verify whether it would be possible to take legal action against the proposal after its adoption.
Other MEPs, however, while recognising that the package was not perfect in their view, recognised that if it went to conciliation or the vote was lost in September, the final regulation could end up closer to the Council position than the amendment.
Hare said that, despite the agreement, the legislation could still potentially be damaging for the food industry.
"Larger companies will benefit from harmonization across all member states but for smaller companies the regulation could be hard to understand," he said.
Moreover, since the registration process still requires the compilation and submission of a dossier, the costs associated with this (as much as £100,000 (€147,000) per product, plus possible fees for EFSA to review it) could be prohibitive for small and medium enterprises.