Nearly one-third of 14-year-olds fail to reach the required standards in English, maths and science – a worse performance than last year, according to today's key stage 3 Sats results.
The percentage of pupils achieving the expected level 5 in KS3 tests in English and maths combined is 66%, a fall of one percentage point on last year's figures.
And boys' reading abilities dropped, with 62% of boys getting level 5 compared with 65% last year, but writing rose two percentage points to 70%.
In individual subjects, 73% of pupils achieved the expected level in English this year, a one-percentage point drop on 2007.
Slightly more pupils achieved the level in maths, up one percentage point to 77% this year but the numbers in science dropped two percentage points to 71%.
Girls did better than boys at each level in almost all subjects and a higher proportion of them achieved level 5 in English and maths combined (71% compared with 62% of boys).
But boys outperformed girls in science at level 5 (71% girls, 72% boys) and in maths (56% girls, 58% boys) and science (40% girls and 42% boys) at level 6.
More pupils did better at the higher level 6, in this year's tests. In English, the proportion achieving level 6 in writing rose from 34% in 2007 to 36% this year, and in reading from 32% to 33%.
Also, more than half of 14-year-olds achieve above the standard expected for their age in maths – 57% at level 6 or above, up from 56% last year – and the same figure as in 2006.
In science, the numbers getting above average scores stayed static at 41% and 72% of boys got level 5, compared with 71% of girls – down from 73% last year.
This year's Sats have been beset by administrative problems and delays. Some 16% of English results and 6% of maths and science results have still not been sent back to schools.
The department's head of statistics insisted there was sufficient data to produce reliable provisional national results, but regional statistics based on local authorities have not been published today.
Since 1997, thousands more pupils are achieving the required levels overall – 95,000 more at level 5 in English and 54,000 at level 6, 100,000 more pupils at level 5 in maths and 121,000 more at level 6. In science, 68,000 more pupils achieve level 5 and at level 6, 73,000 more.
The schools minister, Jim Knight, congratulated schools on their results.
"KS3 is an important stepping stone to success at further study and life beyond the classroom. It is encouraging that most pupils are achieving at or above the expected standard for their age in all three subjects and almost a third are now achieving the highest levels in maths," he said.
"But I am disappointed by the slight drops in English and science – reversing the rises of last year. We know there is more to do before all of our schools are truly world class and that every young person is reaching their full potential at age 14 and beyond."
He said the reforms set out in the Children's Plan would accelerate improvement.
"We are giving schools the tools they need – massive investment in support for teachers; more support for children's wider needs; and the new secondary curriculum starting next month, which will give them real flexibility over how they teach and the confidence to intervene earlier to give support to the right children, at the right time, in the right way."
But teachers argued that the results could not be relied upon and urged the government to halt Sats and review assessment.
Christine Blower, acting general secretary of the National Union of Teachers, said: "It is understandable why the government has chosen not to publish the provisional local authority figures for KS3, given ETS failures.
"However, it is puzzling that the KS2 figures have been published. No results can be relied upon, particularly in light of the high number of appeals and missing results.
"It is now time to call a halt to the Sats and have a fundamental and independent review of assessment," she said.
Dr Mary Bousted, general secretary of the Association of Teachers and Lecturers, said: "The KS3 tests are an irrelevance. No one will be interested in the results when young people apply for a job.
"In a year when Sats have collapsed under their own weight, cutting the KS3 tests would be an excellent way to reduce the excessive amount of testing our students face."
The shadow schools minister, Nick Gibb, said the government had failed to raise standards.
"The government continues to miss its modest targets and we are left with the unacceptable position that two out of five 14-year-olds are failing to achieve the necessary grades in reading, writing and maths that they will need to be able to achieve at GCSE."
"Only seven in 10 children are now reaching the expected grade in science at age 14. But three years ago when this same cohort was eleven, 86% reached the expected level.
"Clearly something is going very wrong in the first three years of secondary school in this vital subject."
The Liberal Democrat's children spokesperson, Annette Brooke, said it was time for Sats to be scrapped.
"It's a disgrace that on the day the results have been published, many schools will still not yet have received their marked papers.
"The shambles surrounding the marking of this year's tests undermines the credibility of these results. The government must waive the re-marking costs to schools for this year's exams," she added.
The Association of School and College Leaders' general secretary, Dr John Dunford, said: "Far too much is made each year of a percentage point or two up or down in the KS3 results… what is important is that the trend is upwards, reflecting the rising standards in schools across the country.
He said it was a shame the marking controversy had overshadowed pupils' and teachers' hard work and the cost of the operation would draw into question the value for money of KS3 tests.