A third of pupils starting at secondary school this term have not reached the expected standard in both English and maths, figures obtained by The TES reveal.
The published test results for 2003 show that 75 per cent of pupils gained level 4 in English and 73 per cent in maths.
But the Department for Education and Skills has revealed that only 66 per cent of pupils have gained level 4 in both subjects, a similar figure to last year.
Phil Willis, Liberal Democrat education spokesman, said that key stage 2 results were stagnating partly because schools were concentrating only on hitting individual subject targets.
He said: "Schools do not have the freedom to say 'this child is likely to hit level 4 in English but not in maths, so let's give them more help with their maths'. They are working to a centralist agenda, not a child-centred agenda."
David Hart, general secretary of the National Association of Head Teachers, said: "If we are going to have targets at all, a target which combines English and maths is far more meaningful than separate scores."
Alan Smithers, professor of education at Liverpool university, said that level 4 was originally defined, when the national curriculum was introduced in 1988, as the level expected of the average child. Any attempt to get high proportions of children performing to this level was therefore very ambitious.
The literacy and numeracy strategies had achieved a great deal but ministers would do better now to concentrate on ensuring pupils got a good foundation in English and maths in the early years, Professor Smithers said.
Kevan Collins, director of the primary strategy, told The TES that the Government was trying to discover why some pupils who achieved level 4 in only English or maths. This year's statistics show that if every child who earned a level 4 in just one subject were to achieve it in both, the joint figure would have been 81 per cent.
At key stage 1, the figures show that 78 per cent of seven-year-olds got level 2 in reading, writing and maths in 2003, compared to 84 per cent, 81 per cent and 90 per cent last year.
Meanwhile, a researcher has claimed that the key stage 2 targets for English are unlikely to be met because children do not understand how to use the apostrophe or punctuate correctly.
Caroline Wassouf, of Manchester Metropolitan University, followed 96 pupils in the Stockport area for 15 months from September 2000 and found that many did not understand the punctuation rules necessary to gain a level 4.
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