The findings are likely to embarrass ministers who plan to release research today proving that their new national literacy strategy is raising standards in reading.
The Scottish study, also funded partly by the Government, suggests that children's progress is much more rapid if different teaching methods than those favoured by ministers are used.
David Blunkett, the Secretary of State for Education, has laid down teaching methods which schools should use in the daily literacy hour introduced in primary schools this term. The methods are not compulsory, but schools will be reprimanded for not using the techniques if their results do not come up to scratch.
But research from St Andrews University reveals that "analytic phonics", the method recommended for the literacy hour, is much less successful in improving reading than "synthetic phonics".
The study, commissioned by Clackmannanshire Council and funded partly by the Scottish Office, involved 300 pupils and 13 classes in eight schools. Researchers Dr Rhona Johnston and Joyce Watson divided them into three groups. The group taught with synthetic phonics rather than methods advocated in the national strategy far outperformed the other groups.
After 16 weeks, children in the former group had reading ages which were, on average, seven months ahead of theirchronological ages, while the latter groups had fallen slightly behind their chronological ages. By the end of the first year, the synthetic phonics group was a year ahead of its reading age and 14 months ahead in spelling.
In analytic phonics, children start with a word and break it down into letter sounds - "cat" becomes c-a-t - and they concentrate on the initial letters of words. In synthetic phonics, they move much faster - they are taught the 42 letter sounds at six a day in eight days. At the same time, they are taught to identify letters in the initial, middle and final positions in words and to sound and blend words using magnetic letters.
Dr Johnston said: "Synthetic phonics is staggeringly effective. We have been using the methods of the national literacy strategy in Scotland for three years. Three years ago, we would have said that we were very pleased with it. Now we are saying that you can do much better. The results were best in the most deprived schools and boys benefit just as much as girls."
The project had used the schools' own teachers who received two days' training and had involved no extra resources.
Lorna Spence, head of Deerpark primary school in Clackmannanshire - one of the schools which trialled synthetic phonics - said that the percentage of children reading at or above their chronological ages had risen from under half, to more than 93 per cent. The teacher remained the same.
Her school is in a mining village and nearly a third of the children come from households where no one has a job. Forty-five per cent are on free school meals. She said: "The results were quite astounding."
In England, some primary schools use a commercial scheme, Jolly Phonics, which uses similar methods.Reuse content