The Michelin-starred chef claimed that demonising the drinks instead of focusing on sugar in general was adding to the "minefield" that parents faced when deciding how to feed their family.
He said: "If Jamie's promoting the fact that sugar's bad for you, then it's a great thing, but you can't just put tax on sweet drinks, you've got to put it on everything with sugar.
"I think if you just tax one thing that's going to confuse everybody further because it's actually specifically sugar that's the problem and that means milk and fruit juice too.
"It's become a minefield because there's not been enough transparency."
The chef spoke out as he launched a new Food Preparation and Nutrition GCSE with exam board Oxford Cambridge and RSA.
With the number of pupils taking food technology at GCSE dropping by 20 per cent since 2004, the hope is that Blumenthal will encourage students back into the kitchen, especially boys, with his new syllabus.
Speaking about the current treatment of the subject, he said: "It's shocking that GCSE is optional and it's been dropped at A-level; the most important thing in the world to keep us alive and keep us healthy has been dropped. A-level should be brought back and GCSE should be compulsory."
Blumenthal dismissed the idea that the more "rigorous, scientific" course, which increases theory and reduces practical assessment, would put off the 200,000 pupils that take the subject.
"(Children) are afraid of science because the way it's currently taught is like a lot of subjects: the kids are being treated as sponges, they've got to learn, question nothing and just soak up and it's right or it's wrong."
He said he hoped his brand of molecular gastronomy and "whizz-bang" would bring "discovery, curiosity, adventure, playfulness" back into an education system that was "still in the Victorian period".
Blumenthal also hoped that an understanding of nutrition could reduce the UK's obesity crisis.
"Obesity and diabetes are rocketing - and eating disorders - and this will help definitely on several levels.
"One is the bacteria in our guts. Because we're eating food that is so processed, we're losing the good bacteria, for example kids are becoming immune to antibiotics and the bacteria that helps protect us against becoming obese is not being fed and is dying off. (This course helps) understand diet and dealing with sugar, it covers everything."
OCR said the new syllabus "incorporates science, nutrition and cooking skills and links to global issues such as food shortage", with Blumenthal suggesting insects as a future source of protein.
"We're happy to eat a prawn that's been kept on a murky bed of its own excrement, so eat a grasshopper! It's just that we're not used to it, we're used to more packed and processed food and we don't want to see where the food's come from.
"Rather than gloss that under the carpet, let kids see and then decide...Kids don't have to go to an abattoir but there are very different levels of farming, like big commercial farms, that they should know about."
Blumenthal's new GCSE will be introduced in the next academic year.
