The court heard two parallel cases, one from the National Association of Health Stores and Health Food Manufacturers Association, which between them represent almost 600 companies, and the other from health campaign group the Alliance for Natural Health.
All of the organisations have been fighting the introduction of the 2002 food supplements directive, scheduled for this August, as they claim that the list developed by the European Commission to harmonise the nutrients and nutrient sources permitted in supplements on the EU market leaves off around 300 ingredients currently used in products sold in the UK.
The debate has become a high profile affair in the UK, attracting celebrity campaigners who have repeatedly petitioned the government. The parliament's house of commons heard many of the same arguments presented at the ECJ yesterday in an afternoon debate led by the Conservative party, which appears to have had some effect on reducing the opposition's presence in Luxembourg.
"We had expected the UK government and we only found out 15 minutes before the hearing started that they wouldn't be there," said David Adams, director of the Health Food Manufacturers Association.
Along with Portugal, the UK had filed its opposition to the case in Written Observations, making its absence surprising.
David Hinde, solicitor and ANH legal director, said: "Given the vigour with which the UK government resisted this application at the Judicial Review stage, it was extraordinary it did not now think the issue sufficiently important to warrant being represented at the ECJ to make oral submissions."
"The question inevitably arises whether this signifies a change of attitude on their part and a retreat from their previously bullish position about the legality of the directive."
Opposition, represented by the European Commission, the Council of Ministers and the European Parliament and one EU member state, Greece, did not appear to rebut any of the major arguments presented by the trade associations.
The senior judge at the hearing, Advocate General Geelhoed, posed two questions, one related to the process of dossier submission and the other to the origins of the annexes.
He is reported to have called the procedure for adding nutrients to the positive list "as transparent as a black box".
Dr Robert Verkerk, executive director of the ANH, said: "It was remarkable that the vast majority of points that we had gone to great length to show the Court were not countered in any effective way by the opposing parties."
However David Adams noted that challenges to EU directives are extremely rare.
The Advocate General said he would deliver his opinion on 5 April. This is "influential but not the verdict", according to Adams. The Court is expected to give its judgment in June, shortly before the deadline for submission of dossiers for adding nutrients to the positive list.
Manufacturers of products not on the list must submit scientific dossiers to the European food safety authority by mid-July in order for them to remain on the market.