Some 74 per cent of 14-year-olds achieved at least a level 5 in English, compared with 71 per cent last year. In maths, the comparable percentage rose from 73 to 74 per cent, while in science the proportion of pupils at level 5 or above rose from 66 to 70 per cent.
The proportion of pupils attaining level 5 in teacher assessment for information and communication technology also rose, from 67 to 69 per cent.
The most striking feature of this year's results was the improvement in boys' writing. The proportion achieving level 5 rose from 59 per cent in 2003 to 65 per cent in 2004 and 70 per cent this year.
However, girls increased their lead over boys in reading, which means the gap between the sexes was unchanged for English as a whole. For the subject overall, 80 per cent of girls achieved level 5 or above, compared with 67 per cent of boys.
For both English and maths, ministers wanted 75 per cent of 14-year-olds to achieve level 5 by last year. Their target is 85 per cent by 2007.
Individual school results have yet to be released officially. But ministers said all 13 academies where pupils sat the tests this year had improved their results.
Jacqui Smith, the school standards minister, said pupils were now reaping the benefit of the Government's introduction of the KS3 strategy in 2001.
The Secondary Heads Association put the improvements down to schools' hard work and the fact that teacher shortages had eased in the past three years.
However, both SHA and the National Union of Teachers renewed their calls for a reduction in the number of tests and exams that pupils face.