Most variation between schools' test results is caused by factors such as deprivation, previous attainment and special needs rather than any difference in effectiveness, a Department for Education and Skills analysis of exam results found.
Unlike Wales, which abolished league tables in 2001, Westminster has put tables at the heart of its standards agenda and used them to set numerous targets for schools.
The report will be seized upon by opponents of league tables as evidence that the Government's insistence on publishing them is unfair to schools and is bad politics. But ministers are unlikely to follow the example of their Labour counterparts in Wales and scrap them. Instead, they hope new school profiles will shift the spotlight away from the publication of raw test scores.
Statistics of Education: Variation in pupil progress 2003, published on the DfES website, said that the use of "threshold" measures such as the number of pupils reaching expected national curriculum level or gaining five or more A*-C grade GCSEs, further distorts the view of schools' performance given by the tables.
Targets are routinely based on threshold measures.
The report said: "If value-added scores are used as an indicator of how effective a school is, it is important to be aware of the potential uncertainty around the figures.
"The school could have been equally effective and yet the same set of pupils might have achieved different results on the same day."
Small differences in test scores between schools or over time should not be interpreted as showing significant differences in effectiveness, it added.
Small schools are also particularly vulnerable to year-on-year fluctuations.
Once background factors are taken into account, more than a third of schools have results which are not significantly different from the national average.
Critics say league tables paint an unfair picture of schools with disadvantaged intakes, a position backed last year by the National Audit Office.
The DfES report said that variations in schools' performance makes up less than a 12th of the unexplained difference in pupils' results once background factors are taken into account.
The report also noted that large concentrations of deprived pupils depress school performance.
Schools where half of the pupils are on free school meals have test results 22 per cent lower than those with affluent intakes.
The predicted difference, based on the national performance of deprived pupils, is just 7 per cent.
The finding will be seized upon by critics of the current admissions system who argue that it allows popular schools to covertly select pupils from affluent backgrounds.
John Bangs, National Union of Teachers head of education, said: "League tables are not only inaccurate, they victimise schools at the bottom. This is remarkably enlightened. This is everything we have always said, and that Wales understood a long time ago. It has just taken a bit of time for the penny to drop over here."
leader 14 www.dfes.gov.uk