A previous measure, which rated schools by how far their pupils' progressed between age 7 and 11, has been abandoned.
The tables show that 80 per cent of pupils reached the expected level 4 in English, 77 per cent in maths and 88 per cent in science.
Orrets Meadow on the Wirral, a special school, topped the contextual value-added table, followed by St Joseph's Junior, Infant and Nursery in Oldham.
Contextual value added gives each school a score based around 100, but takes into account children's prior test scores, gender, ethnicity, age in year, special educational needs, whether the child claims free school meals, their first language, whether the pupil is or has been in care, movement between schools and the area's deprivation rating.
Sandra Blythe, head of Orrets Meadow, said: "We have lots of mainstream colleagues coming in to view our lessons, and the one thing they comment on is the pace of our lessons. It's quick - boom, boom, boom, no messing around.
"What we always say is that most children would be successful with our type of teaching. We have small classes, lots of opportunities for learning, carefully structured work, individual and group lessons and multi-sensory teaching."
Andy Dickinson became headteacher of St Joseph's in Oldham, 10 years after his own father stepped down from the job. As well as the top CVA score in mainstream primaries, all pupils achieved level 4 in all three subjects this year. He said motivating pupils was a key ingredient of the school's success: "Two years' ago we came second in the country in attainment. That doesn't mean anything like as much to me as this.
"I have no problem with standardised tests, but it's the publication of attainment tables which is so misleading to parents because it is all relative. There are schools with superb progress but attainment is low and that saps the soul of the most dedicated teachers."
The concerns about "raw" scores, which do not take into account different starting points, led to the original value-added scores in 2003, which simply compared pupils test scores at 7 and 11. However, the current tweak of contextual value-added scores is unlikely to defuse the growing concern over the target, test and tables culture.
The ongoing select committee inquiry into assessment has found widespread concern among unions, academics and subject associations that the current system promotes shallow learning.
The Dean's Primary, Salford, had the highest overall score with all 26 pupils gaining level 5 in English and science and all but one doing so in maths. South Farnham School in Surrey had the largest cohort, 120 pupils gaining level 4.
KEY STAGE 2 SUCCESS STORIES
Top 10 mainstream schools for value-added (based on contextual scores, with ties broken by the number of pupils eligible)
1. St Joseph's RC Junior Infant and Nursery, Oldham
2. Gateway Primary, Marylebone, London
3. Boundary Primary, Blackpool
4. St George's Beneficial CofE VC Primary, Portsmouth
5. Kingswood Primary, West Norwood, London
6. Cobourg Primary, Southwark, London
7. Clenchwarton Community Primary, King's Lynn
8. Abbey Hulton Primary, Stoke-on-Trent
9. Manor Junior and Infant School, Bilston, Wolverhampton
10. Chesterton Primary, Battersea, London
Top ten most improved schools in England
(judged by rise in aggregate results from 2004 to 2007)
1. Furrow Community School, Manchester
2. Broadwater Farm Primary, Haringey, London
3. Moor Nook Community Primary, Preston
4. Elm Hall Primary, Witham, Essex
5. Chesterton Primary, Wandsworth, south London
6. St Andrew's C of E Primary, Lambeth, London
7. St Joseph's RC Primary, Gateshead
8. Hill Top Primary, Doncaster
9. The Reddings Primary, Hemel Hempstead
10. Lowerplace Primary, Rochdale
Top five schools for proportion of pupils at level 5
(based on aggregate scores)
1. The Deans Primary, Salford
2. South Farnham Community Junior School, Surrey
3. North Cheshire Jewish Primary, Cheadle
4. Combe Church of England Primary, Oxfordshire
5. Walker Primary, Enfield, London.