Two-thirds of schools at the top of the first value-added league tables for primaries, published yesterday, also have test scores for 11-year-olds well ahead of the national average.

The tables identify low-scoring schools doing well with deprived intakes.

But the lack of such schools in the top rank has led some to question whether value-added tables are fair to schools in challenging circumstances.

The tables, which measure the progress pupils make between seven and 11, have been published in response to complaints that unadjusted or raw, scores are unfair to schools with a high proportion of poor children.

But two-thirds of the top value-added primaries have a combined score in English, maths and science which is at least 30 points ahead of the national average.

Critics say the scores are still misleading because children’s backgrounds influence their rate of progress as well as their starting point.

John Bangs, head of education at the National Union of Teachers, said:

“Having value-added tables based on prior attainment is next to useless and adds spurious authenticity. It shifts winners and losers around but is still pernicious.”

But some primaries are pleased with the difference value-added makes.

Schools which are making average progress get a score of 100. Delaval primary in Newcastle has a value-added score of 105.5, the highest in England.

Sandra Marsden, headteacher of Delaval, said: “We wouldn’t be anywhere in the traditional tables. Value-added does provide a balance to the absolute marks that you get at key stage 2.”

Value-added scores also appear to recognise the work of special schools.

Castledean in Brighton takes pupils with moderate learning, communication and behavioural difficulties. None of its pupils achieved level 4 in English, maths or science, but it has the eighth-highest value-added score.

The tables still show the raw scores for the proportion of 11-year-olds reaching the expected level 4.

This year, Werrington primary in Peterborough was top of the level 4 table with 62 pupils all reaching the expected standard in English, maths and science. It was one of 142 schools to get a clean sweep, compared with 179 last year.

At the bottom of the table was Moor Nook in Preston, where 14 per cent of pupils achieved level 4 in English and 20 per cent did so in maths. Cecilia Davies, headteacher, said that 25 of the 35 children who took the tests had special needs. She said: “If children are capable of getting a level 5 they will get it. These tables give the wrong impression about this school.”

For the first time, the proportion of pupils reaching level 5 is recorded.

Combe Church of England primary in Witney, Oxfordshire, emerged as the best-performing primary in this table with all 12 pupils taking the exams reaching this standard.

Richmond-upon-Thames was the most successful education authority, after the City of London which has just one school.

The City of London also tops both the value-added table for education authorities as well as the “raw” scores table based on the percentage of 11-year-olds achieving level 4. Next comes Kensington and Chelsea which is fifth in the traditional tables. Richmond on Thames is joint 14th place for value-added.

The most remarkable rise is Newham which is 12th from bottom in the traditional tables, but has the seventh best value-added score in England.

Hackney, which is bottom of the raw-score tables, is one of 22 authorities with a value-added score of 99.9 matching the national average and putting it in joint 73rd place.

The Isles of Scilly, which has just four primary schools, comes bottom of the value-added table, just above it is North Lincolnshire.

An alliance of local authority chief education officers, headteachers and governors have called for a further shake-up of the tables.

Six organisations have written to David Miliband, the schools minister.

They stop short of saying that the tables should be scrapped, but question the reliability and validity of tests as a tool for creating the performance tables.

Mr Miliband said: “We have always said that we will listen to the views of heads, teachers and parents about how the performance tables can provide a more comprehensive and rounded picture of school performance.”

He said this was demonstrated by the inclusion of value-added scores this year.