The EHPM has today warned of a serious supply shortage for the industry if a deadline for companies applying for permission to process fish oil is not extended.
The hygiene changes, which aim to improve food safety throughout the supply chain, require all businesses processing fish oils, including omega-3, to be officially approved by the companies' local authority.
The criteria, "Regulation (EC) 854/2004 laying down specific rules for the organisation of official controls on products of animal origin intended for human consumption", requires businesses to meet tough health checks to avoid fish contamination with parasites or harmful substances.
A lengthy list of directions to ensure high hygiene standards include making sure surfaces that may come into contact with fishery products must be of suitable material, and specifications for temperature and storage of fish are set out.
Although the hygiene rules were adopted in 2004 by the European Parliament, the EHPM says that the November deadline for certification needs to be extended by two years to allow member state countries to comply with the law.
Chairman Peter van Doorn warned there were still processing factories in the EU which had not completed the certification process because of the time it has taken to bring processing plants up to the required standard.
He said: "The majority of existing fish oil processing facilities in certain countries will not have their establishment registered in time to meet the November deadline due to the heavy costs and procedures that this entails.
"This situation is likely, therefore, to have an impact on the whole EU fish oil supplement industry - there is a real risk of a shortage of fish oil sources."
However, the EHPM was unavailable to indicate how many businesses are currently uncertified prior to NutraIngredients.com being published.
Although vegetarian options are available as a source of omega-3, fish oil is widely regarded to be the best source of DHA (docosahexaenoic acid) and EPA (eicosapentaenoic acid).
It is not yet known how the rules might affect the European omega-3 market, which according to Frost & Sullivan was worth around €160m (£108m) in 2004 - and is expected to grow at around 8 per cent a year until 2010.
The hygiene rules, which came into force in May, also state that a health certificate is needed to import fish oils for use in foods.
According to EHPM the majority of fish oil used in the production of omega 3 and other fish oil supplements are sourced from non EU countries, such as South America, Canada, and Morocco.
The trade association fears that these countries will not be able to adapt their current health certificate by the requested deadline due to lengthy paperwork procedures.
Van Doorn added: " The deadline extension will allow time for countries to conform to EU rules.
"Sustainability for our raw materials is an important issue.
We are working to support and promote the food supplement industry, so that it can grow."
The potential benefits of omega-3 supplements are said to be wide and varied, with a clinical study just last month linking the fatty acids to having a positive effect in combating depression and agitation symptoms associated with Alzheimer's disease.
Doses of omega-3 have also been linked to weight loss, cardiovascular health, infant development and joint health.