The flood of dossiers, rising from less than 30 submitted by mid-June to more than 500 by yesterday's deadline, was the result of negotiations between trade bodies and UK authorities, leading to more lenient requirements for their submission.
However David Adams, director of the Health Food Manufacturer's Association (HFMA), warned that the dossiers merely offered short-term derogation from the directive.
"After this it depends on whether they actually get approval from EFSA," he said.
The directive's positive list of permitted ingredients does not include an estimated 270 sources commonly used to make vitamin and mineral supplements currently available on the UK market.
Industry bodies and consumers had feared that the 2002 directive would result in around 5,000 products containing these ingredients being removed from sale.
However under the derogation process, supplements will be allowed to stay on the market provided that a dossier of information on their safety has been submitted to the European Food Safety Authority via a member state agency prior to yesterday's deadline.
There had been concerns that most companies could not afford the significant costs associated with completing dossiers. However extra funding from the UK government, largely negotiated by the Health Food Manufacturer's Association (HFMA), raised
Companies were also encouraged by a letter sent out by FSA in June that said it would accept all dossiers submitted with "basic information" including the length of time on the market and whether there were any reports of associated adverse effects.
However in an interview last month, David Adams, noted that this "still leaves the longer-term issue of how and whether to fund the very extensive extra work that is likely to be required for dossiers to obtain final approval from EFSA."
FSA is not evaluating any of the dossiers it receives, but merely acting as a postbox to the Commission.
"We are relying on available data and not creating any new data for these dossiers. As some are not particularly full, it is quite possible that EFSA will ask detailed questions that require further scientific work," Adams explained.
Well-known supplements on the list include selenium yeast, tin, manganese and vitamin K2. The rest can be viewed here.
The FSA said the "great majority of food supplements people take will continue to be freely available to UK consumers".