The results will concern ministers who pledged to protect rural schools from closure as part of their attempts to defuse complaints that the Government was out of touch with those living in the countryside.
Eleven-year-olds in schools with 10 or fewer pupils in their year group gain worse results in English, maths and science than those in bigger schools. Seven-year-olds in such schools are also less likely to reach the expected key stage 1 level in all subjects.
Only 59 per cent of 11-year-olds in small schools achieve level 4 in English compared to 75 per cent in all schools. In maths the figure is 56 per cent compared to 72 per cent and in science the gap is bigger - 66 per cent compared to 85 per cent for all schools.
The difference in performance was revealed by schools minister Stephen Timms in a parliamentary answer. He said that for schools with 10 or more pupils in each age group, school size "appears to have little significant effect" on results.
One reason for the small schools results according to the Department for Education and Skills, was that special schools made up a great proportion of the sample. Other factors such as mixed-age classes also have an effect.
Mike Carter, vice-chair of the National Small Schools Forum, said that the figures gave a distorted picture of performance because of the low number of schools with such small cohorts.
He said that Office for Standards in Education research showed that the quality of teaching in small schools was better than average and that this, along with the generally positive experience of parents, was a better reflection of small schools' achievements.
"We would accept that the smallest have the greatest difficulty but small schools make a great contribution to educational standards," he added.
Chris Girdler, assistant secretary at the National Association of Headteachers, said: "This is a surprise. Schools of this size do not have their results published in the performance tables, but anecdotally one's impression is that they do incredibly well."
A spokesperson for the Department for Education and Skills said that the Government acknowledged the extra pressures faced by small schools.
It is providing pound;80 million through the small schools fund which runs until 2004, to help with administration and the cost of buying computers.