Just over half of boys begin secondary school with the expected skills in reading, writing and maths, compared to almost two-thirds of girls.
The new figures from the Department for Education and Skills showed that the gender gap widened last year.
In 2005, 51 per cent of boys reached the expected level 4 in reading, writing and maths, compared with 63 per cent of girls.
There was a one percentage point drop in boys' scores compared to 2004 and a one percentage point rise for girls.
Since Labour came to power in 1997, the percentage of 11-year-olds reaching level 4 in all three subjects has risen.
In 1997 results, 38 per cent of boys and 49 per cent of girls reached level 4 in all three subjects.
The statistics released this week follow a furore last month, when the Conservatives accused the Government of not publishing the combined figure until asked.
Now the Government has published figures showing boys' and girls'
achievement in six different combinations of subjects this year.
These show that 89 per cent of boys and 91 per cent of girls achieve level 4 in at least one out of English, maths and science. And 67 per cent of girls and 71 per cent of boys achieve level 4 in English, maths and science.
The figures are higher than those in which English is broken into reading and writing because a pupil can reach level 4 in English without reaching level 4 in writing, if their reading score is high enough to bring the average up.
The Government's targets are for 85 per cent of pupils to reach level 4 in English and in maths.