The consumer group found most companies have removed health claims for supplements that have failed to gain EU approval, but said a small number are still using "ambiguous" packaging to promote products.
Which? said three products - Bioglan Probiotic capsules, Bimuno Prebiotic powder and Seven Seas Cardiomax - made unproven health claims on their packaging such as "helps maintain digestive balance" and "for a healthy heart".
Which? said: "Confused consumers are likely to think the benefits of these products come from the main ingredients, as heavily advertised on the packaging, which could lead to people wasting money."
Bioglan told Which? it had changed its packaging to comply with the EU's decision, while Seven Seas said it was redesigning CardioMax packaging. Bimuno said it believed its claims were substantiated.
Which? executive director Richard Lloyd said: "It's worrying that some manufacturers aren't playing fair on the packaging of food supplements, making claims which could leave shoppers out of pocket."
The Health Food Manufacturers' Association rejected the findings.