Four in 10 boys aged 14 in England did not attain the level they were expected to in last year's national curriculum tests, final results show.
How results have improved under the Labour government
In the Key Stage 3 Sats, 60% of boys achieved Level 5 or above last year in English and maths and science.
Girls did better - 67% making the grade - so the overall average was 64% in the tests, which indicate how well they will probably do in GCSEs in 2009.
In the individual subjects the results fell short of the government's targets.
It had hoped that 85% would be on Level 5 or above in English and maths and 80% in science.
Ministers are promising that pupils will get extra, targeted help
The results - compiled and checked by schools for official performance tables - showed 74% making the grade in English, 76% in maths and 73% in science.
Those were an improvement of one percentage point on the 2006 results in English and in science.
The maths result was one point worse than in 2006, but that year had seen a three point rise on the previous year.
There was a gap of about 20 percentage points in each subject between the attainment in the most deprived and least deprived areas of the country.
Schools Minister Jim Knight said some schools had made excellent progress in recent years.
"It's crucial that other schools learn from their example - the first three years in secondary school should provide pupils with a firm foundation to the rest of their academic life and is not a time for coasting," he said.
"The Key Stage 3 results give a good indication of how pupils will achieve at GCSE and I am impatient to see more progress made and see more pupils reach the levels expected for 14-year-olds.
"To help this happen in Key Stage 3 maths from this September there will be new innovative Key Stage 3 mathematics lesson materials available for schools, the new curriculum will allow greater flexibility, we have increased the teacher training bursary for maths teachers to £9,000."
A National Centre for Excellence in the Teaching of Mathematics had been set up and there was a national strategy providing continuing professional development for teachers of maths focused on raising pupils' attainment.
Mr Knight said he hoped the new Diplomas, being taught in some areas from September, might prove to be the key to turning young people back on to study who currently at Key Stage 3 looked ahead and did not see the traditional route of GCSEs and A-levels as being for them.
Shadow children's secretary Michael Gove said the figures showed that tens of thousands of pupils who had reached the expected level when they were 11 had failed to progress at all in the next three years: 7% in maths, 11% in English and 17% in science.
"We urgently need to deal with this problem," he said.
"We need better discipline and more setting so the brightest children are stretched and those that struggle get the targeted help they need."
Government statisticians calculated that less than half the pupils reached Level 5 in each subject in 279 schools out of a total of 3,082.
The target is to reduce this to zero by this year.
Liberal Democrat schools spokesman David Laws said ministers were now set to miss that "unambitious" target too.
"In a majority of schools, more than a fifth of pupils are failing to reach the government's benchmark in maths.
"With such limited progress, it is clear that the government must target the disadvantaged young people who underperform when they start education and then seem to fall further behind," he said.
The general secretary of the National Union of Teachers, Steve Sinnott, said one reform Mr Knight should introduce was the removal of the current testing and performance table regime.