The European Court has decided to tighten rules on the sale of vitamins and minerals.
An estimated 10m Britons take vitamin supplements
The proposals could ban around 200 supplements from sale and put restrictions on the upper limits of vitamin doses.
Some health experts wanted to see vitamins and minerals controlled in the same way as conventional medicines.
But critics argued the new rules were unnecessarily restrictive, and would deny consumers choice.
Under the EU Food Supplements Directive, due to come into effect in August, supplements will only be able to include vitamins and minerals taken from an approved list.
Minerals not currently on the approved list include tin, silicon, nickel, boron, cobalt and vanadium.
However, manufacturers of products already on the market will have until the end of December 2009 to change any of the banned ingredients to ensure that their product can continue to be sold in the future.
Also, the Alliance for Natural Health (ANH) said it interpreted the ban as applying only to synthetically produced supplements - and not to vitamins and minerals normally found in or consumed as part of the diet.
The ban had been challenged by the ANH, the Health Food Manufacturers' Association (HFMA) and the National Association of Health Stores (NAHS).
They argued the legislation would be too restrictive, and would threaten thousands of perfectly safe products.
The directive was first approved by EU governments in 2002 and was designed to tighten controls on the growing market in products sold under the health food heading - natural remedies, vitamin supplements and mineral plant extracts.
The HFMA and the ANH argued the directive was an unlawful restriction on freedom to trade, that implementation would impose an unnecessary burden on British business and there are no reasons to believe it is necessary to protect consumers' welfare.
After reviewing the evidence presented by both sides, European Court of Justice Advocate General Leendert Geelhoed said in April that the directive infringed legal guidelines in his opinion.
However, the court pointed out that certain restrictions could be justified by the protection of public health and considered the measures in question to be necessary and appropriate for the purpose of achieving that objective.
The British Dietetic Association backed the new plans.
It is concerned about patients admitted to hospital suffering liver failure and severe stomach problems after taking high doses of vitamins.
It said in some cases the supplements are preventing people getting the correct treatment for other chronic illness.
Spokeswoman Ursula Arens said consumers should not be greatly affected by the changes.
"About 99% of products will not be affected."
The ruling was also welcomed by Sue Davies, of the consumer magazine Which?.
She said: "It will ensure that products are safe, that they contain forms of vitamins and minerals that offer some benefit, and that they are clearly labelled."
Peter Aldiss, managing director of Holland and Barrett, said he was very disappointed by the decision.
"There are hundreds of nutrients which are already very safely on sale with very strict laws in the UK.
"This directive purely just takes those nutrients out of the reckoning - they're perfectly safe and they've been on sale for decades."
David Adams, director of HFMA, said the Prime Minister, who currently holds the EU Presidency, should get the legislation rewritten to allow the UK to include products on the market which would otherwise lie outside the list - a call echoed by the Conservative Party.
The ANH said its lawyers had interpreted the directive's restrictions to apply only to minerals and vitamins from synthetic sources.
Public Health Minister Caroline Flint, said government was concerned that some of the provisions in the Directive could be "unduly burdensome", particularly for small companies making these products.
"We have provided resources to help industry and small businesses supply the evidence necessary to allow their products to continue to stay on the market for the time being. This doesn't require them to do any new testing or provide new data at this stage.
"The directive will also set maximum levels of vitamins and minerals in food supplements. We believe that any maximum dosage level should be based on scientific evidence. We will work with other member states and the European Commission on this basis."
It will be possible to add products to the approved list and none will be removed unless they are proved to be unsafe.