Too many pupils of average ability were entered for the test for brighter children, Rose Clesham, the National Assessment Agency's principal officer for key stage 2 and 3 science, told the ASE conference.
The sharp increase in the number of pupils taking the harder paper was the major reason for the two percentage-point fall in the proportion of 14-year-olds reaching the expected level in science last year, she said.
Official figures show the percentage entered for the harder test rose to 43 per cent in 2004 from 36 per cent the previous year. More than 8,500 pupils who sat the top paper failed to get level 5, the expected level, compared to fewer than 1,700 in 2003.
Teachers have to decide which of two tests each pupil should sit. The lower-level paper offers pupils the chance to gain levels 3 to 6, while the higher paper is intended for level 5 to 7 pupils, although pupils who just miss out on level 5 can be awarded a level 4.
Ms Clesham also revealed that teachers will be banned from helping pupils with spelling in key stage 2 and 3 science tests after some teachers were found to be filling in technical words for their pupils.
Ambiguous rules had allowed teachers to give assistance to pupils who find spelling difficult.
Now markers will be told to "err on the generous side" and award marks where meaning is clear, even if the spelling is poor.