The research, covering nearly 20,000 pupils, suggests that the shift of focus from primary school is beginning to have an effect.
If mirrored nationally, the results will be used by ministers to push forward the shake-up of secondaries, which the Office for Standards in Education claimed last week were letting too many pupils slip behind.
Education Secretary Estelle Morris has made clear that her tenure should be judged by key stage 3 improvements.
As these latest survey results emerged, one of the main architects and director of the maths strategy announced her retirement. Anita Straker, former head of the numeracy strategy, will remain a consultant on both initiatives.
She said: "Eighteen months ago, heads were resentful about the strategy. Now they are saying it is useful stuff. The real gains will come in the 2004 tests."
Test scores from just over 100 schools surveyed showed increases in all three papers. In English, 70 per cent of teenagers reached level 5 or above - up six percentage points on 2001. If the national picture is similar, this year's results would break a three-year stagnation in the subject. The rise was achieved despite criticism of marking standards. About a quarter of schools in the survey said they had sent back scripts for remarks.
Schools reported an average increase of four percentage points in maths and science, which would also bring the proportion of pupils achieving the expected levels to 70 per cent.
The survey bodes well for the first KS3 targets in 2004. By then, three-quarters of 14-year-olds should achieve level 5 in maths and English. Most schools in the survey hit their individual targets.
A pound;4,500 government grant to schools for booster classes was credited with helping borderline pupils scrape a level 5, despite some complaints that it had arrived too late.
Marie Getheridge, head of Writhlington school in Avon, said a fifth of children who were heading for level 4 reached level 5 after booster classes. At Arnold Hill school in Nottinghamshire, 18 out of 20 pupils who attended extra science classes achieved the milestone.
The English and maths strands of the KS3 strategy have been in place since September. While they are focused mainly on Year 7, a number of heads felt the improvements in teaching had spread to Years 8 and 9.
Time spent on the 3Rs in primary school was also bearing fruit, according to some schools. The 14-year-olds sitting the test this year had two years of the literacy strategy and one year of the maths hour.
Despite the positive picture painted by the survey, there were still huge differences in individual schools' results. Almost 100 per cent of pupils attending the grammar schools in the poll achieved level 5 or above. At the other end of the scale, one Birmingham school failed to get half its pupils to the expected level in any subject.
KS3 test results will be included in the league tables for the first time this year, but most respondents said GCSE results were still the measure schools would be judged by.
Tony Neal, president of the Secondary Heads Association, said schools were better at setting individual targets for pupils and this was beginning to make a difference.
"Teachers are stretching youngsters and the comparison of KS2 and KS3 data in the performance tables will give a better idea of the contribution secondary schools make to pupils' progress."