Campaigners including chef Jamie Oliver have been calling for a levy of 20 per cent to be included in the Government's upcoming Childhood Obesity Strategy.
It is estimated that a tax of 7p per regular sized can could generate an additional £1bn a year to fund children's health programmes.
But Martin said the plans were based on ‘fashion, not science’ and that sales of sugar-free drinks were already rising across his 950-strong pub chain.
Almost 60 per cent of soft drink, coffee and tea sales in Wetherspoon’s pubs are sold as sugar free, the company claimed.
Martin said: “In my opinion the figures show that taxing sugar in drinks is illogical unless you go further and tax desserts, chocolate, birthday cakes and other products that contain sugar.
“Eggs, for example, were regarded as unhealthy for decades, but the advice has since been reversed. Had the government imposed a tax on eggs, an injustice would have been compounded.
“Since vast areas of pseudo-medical advice concerning food have been overturned in recent years, legislators should tread warily before imposing extra taxes.”
Martin's comments follows reports that David Cameron has scrapped plans to introduce the sugar levy.
The Prime Minister will instead use the threat of the tax to pressure companies in to lowering the sugar content of their products, The Telegraph has claimed.
Over 130 restaurants including Leon, Abokado and Jamie’s Italian have already raised £50,000 for children’s health programmes since introducing a voluntary 10p tax.