This summer's general GCSE science and additional science papers amounted to a "collective falling short" of expectations and were plagued by inconsistent standards between the three exam boards, Isabel Nisbet, chief executive of Ofqual, said.
Failings in the exams, which were sat by more than 800,000 15 and 16 year olds, came despite repeated warnings from the watchdog that examiners ought to place "more severe" demands on pupils because questions had become too easy.
Problems with the papers date back to 2008, when the watchdog told examiners to create new versions of the course to be taught in 2011, with the current exams to be made more difficult in the intervening period.
Earlier this summer Ofqual rejected the 36 new science GCSEs drawn up by exam boards because the courses were still too easy.
The regulator believes questions should be made more difficult and that "disparities" in standards between Edexcel, AQA and OCR, England's three exam boards, must be eliminated.
It said this year's papers failed to address the existing problems with the qualification, but admitted there had been some progress since last summer, when questions included "Which of these is bigger than our galaxy – the Universe, the asteroids, the Moon or the Sun?".
Last year students were also required to clarify whether tobacco is a legal drug, an illegal drug or a prescription drug, and whether beer is produced through the process of fermentation, desalination, ignition or combustion.
Ms Nisbet told the Times Educational Supplement: "If you asked me 'Is GCSE science good enough?' I think the answer would be no.
"I think we have made some progress in toughening up the standards and reducing the disparities but we still have a bit to go."
The number of pupils sitting the two combined science courses dropped sharply this year, while those taking individual papers in biology, chemistry and physics rose by almost a third.
Ms Nisbet added that students should not be disheartened by attacks on the exams which she said were "fairly and consistently marked" and "rigorously checked".
She said: "They should not feel devalued by what has been a perfectly legitimate, finely tuned criticism at a level of sophistication which many countries would just not recognise."
OCR and Edexcel said their new specifications would act on the issues raised by Ofqual. AQA said it wanted Ofqual to take a "tougher stance" after it was told to make exams easier in 2008, to bring it to the level of other exam boards.
--By Nick Collins,27 Aug 2010