While pupils showed signs of improvement in maths at key stage 3, science scores dropped. Seventy-three per cent of 14-year-olds achieved level 5 or higher in maths, up two points on last year. However, there was a two-point drop in science, to 66 per cent.
And while there was a six-point rise in the proportion of pupils gaining level 6 or higher in maths, to 52 per cent, there was a six-point drop in science, to 34 per cent.
The release of English results at key stage 3 has been delayed because of marking problems. No date for publication has yet been given.
David Miliband, school standards minister, said one explanation for the "unexpected" science results was that more pupils than usual were entered for the higher tier tests, which were more difficult. "We are looking into why it might have happened, we are talking to schools about it," he said.
Peter Cotgreave, director of pressure group Save British Science, said the science results were "very worrying" and blamed a shortage of good teachers. "We cannot expect to enthuse kids and get them through their tests if we have not got people who know and enthuse about the subject themselves," he said.
He said ministers needed to act to reverse the situation. Low achievement at primary school and early in secondary school would mean fewer students taking science A-levels and degrees and an even greater shortage of science teachers in future.
Since 1997, the proportion getting level 5 or better in maths has risen by 13 percentage points, while in science it is up by just six points. Girls continue to outperform boys in both subjects.
But some of the traditionally lowest performing local authorities have made the biggest strides in standards in the two subjects. Nottingham and Southwark made the most improvement in KS3 maths, with the percentage of pupils hitting the benchmark up seven points, followed by Bradford with a six-point rise and Brent, Kingston-upon-Hull, North-east Lincolnshire, Rochdale, Slough and Sunderland all improving by five.
In science, Warrington's results rose three points, followed by Tower Hamlets by two, and Bath and North East Somerset, Croydon, Nottingham, Slough and Wokingham all on one point.