The tests, which included runner beans, spring onions and cucumbers, found seven of the 17 manufacturers failing to meet the minimum statutory germination rates set by the Vegetable Seed (England) Regulations 2002.
The magazine said Simpson's Seeds' runner bean 'Hesta' performed the worst — with a 41 per cent success rate — while Unwins' spring onion 'White Lisbon' was also highlighted with 57 per cent.
But some of the companies involved have questioned the reliability of the data. Mr Fothergill's Seeds performed relatively well in the trial, with 84 per cent germinating, but marketing manager Ian Cross said: "I think Which? just like getting their name out there, it makes great news and is good publicity.
"We take quality very seriously and if we had the number of complaints we would expect from those results then we would certainly do something. It is hard to say what we could do any better."
The worst performer in ornamental seed tests was Unwins' Geranium 'Glory of Seville,' 73 per cent of which did not germinate. Ornamentals have no legal minimum rates.
An Unwins representative said: "The reality is that although such results, on the face of it, appear disappointing, Gardening Which? does not produce any information on the testing methods it applies. Such lack of transparency would not stand up to scientific scrutiny."
Unwins head of horticulture Mark Fletcher welcomed the survey and said its new Gro-sure range aims to improve the market.
Gardening Which? head of research Richard Gianfrancesco said he tested using International Seed Testing Association (ISTA) rules and labs.
Overall, Gardening Which? said there had been an improvement on 2007 seed tests.