The opinion from the Advocate General of the European Court of Justice is not legally binding but the final ruling, expected in July, reflects the senior judge's views in the majority of cases.
The directive, passed in 2002, threatens up to 5,000 common products on sale in the UK, according to industry assocations that brought the case against the European Commission.
Under the new law, only vitamins and minerals on an approved list can be used in supplements. There will also be restrictions on the upper limits of vitamin doses, still to be set by European authorities.
The Health Food Manufacturers Association (HFMA) and the National Association of Health Stores (NAHS), as well as health campaign group the Alliance for Natural Health, whose similar case was also heard by the European Court at the January hearing, say that these rules will affect more than 200 nutrients used in specialist supplements on the UK and some other European markets for many years, which are not on the directive's 'positive' list of permitted substances.
While Advocate General Geelhoed said the principle of an approved list was valid, he found that the directive infringed basic principles of law.
He wrote: "The Directive infringes the principle of proportionality, because basic principles of Community law, such as the requirements of legal protection, of legal certainty and of sound administration have not been properly taken into account. The directive is, therefore, invalid."
He also found it to lack appropriate and clearly defined rules for what should be allowed on the list of permissible health food supplements.
Commenting on the problems surrounding the dossier submission process, the judge said: "In short, this procedure, in so far as it may exist and in so far as it may deserve this title, has the transparency of a black box: no provision is made for parties to be heard, no time-limits apply in respect of decision-making; nor, indeed, is there any certainty that a final decision will be taken."
"The procedure therefore lacks essential guarantees for the protection of the interests of private applicants."
Philip Tod, spokesman on health and consumer protection at the European Commission, told NutraIngredients.com that the Commission could not move until the final verdict is reached.
However he added: "It is not unprecedented for the court to not follow the advocate general's opinion. It could still find in our favour."
"There are a wide range of ways in which the court can reach its decision. It may just give an interpretation of the directive," he said.