Voluntary tests for Years 7 and 8 pupils are designed to demonstrate progress made since the national tests taken by 11-year-olds in the last year of primary school.
However, at St Mary's C of E primary school, in Surrey, where bright 11-year-olds took both the national test papers and the Year 7 optional tests, huge disparities between the results were found.
Eight of the 11 pupils secured a very good level 6 in the optional test - the highest grade. Yet in mock national tests, 10 pupils achieved level 5 and one achieved a level 4.
Headteacher Cary Neef said: "I was staggered when I saw the results. One pupil who was level 4 was just marks away from a level 6 in the Year 7 optionals.
"If this 'easier' test is taken at the end of the first year in secondary, it looks like a pupil has jumped two levels."
To achieve a level 6 in the key stage 2 tests, pupils must be entered for an extension paper. In 2001, 60,000 pupils sat the extension paper but less than half a per cent gained the level. The papers will be replaced by starred levels from 2003.
Ms Neef said she only put two of her pupils in for the test because she knows how difficult it is.
Doubts about comparability were also raised last year when many 12-year-olds in catch-up classes failed the key stage 2 tests but gained a level 4 in the optional test.
Millions of pounds has been spent on the Government's KS3 strategy trying to boost performance in the early years of secondary school.
The optional tests, which teachers mark, were taken by about 200,000 pupils this year.
Earlier this year, Estelle Morris, the Education Secretary, said there was evidence that the overhaul of lessons in the middle years, which began in September 2000, was having an effect.