The secondary test information will be published separately from GCSE scores in December for the first time, increasing pressure on teachers and heads to raise 14-year-olds' scores.
Ministers claim they have made the change to emphasise the importance of key stage 3, which underpins pupils' GCSE success.
But the National Union of Teachers, which is to ballot members on a boycott of all key stage tests, said the move would strengthen support for such action.
Eamonn O'Kane, general secretary of the National Association of Schoolmasters Union of Women Teachers, said the use of tables created hostility to the tests.
He added: "I find it hard to understand why there is this obsession with league tables in England, when Scotland, Wales and Northern Ireland are moving in the opposite direction."
David Hart, general secretary of the National Association of Head Teachers, said: "I'm totally appalled. The Government's position on league tables is undermining its drive to raise standards."
Questions are being asked, too, about the reliability of test data, particularly in key stage 3 English. Markers complained on The TES website about the difficulties they had in applying the mark scheme this year.
Schools also complained of big changes in English KS3 test results, though the test regulator insists the scores are reliable.
Mary Bousted, general secretary of the Association of Teachers and Lecturers, said that the move also contradicted government proposals to tailor education to the needs of individual children.
John Wilks, general secretary of the London Association for the Teaching of English, said: "The more status the tests have, the more they constrain teaching."
Margaret Morrissey of the National Association of Parent Teacher Associations, said that parents wanted information on individual schools, but not more league tables which would just add to the pressures on youngsters.
A Department for Education and Skills spokeswoman said: "The decision reflects the importance of KS3 as a critical phase in children's education and the bearing it has on their success at GCSE. Publishing separate tables highlights this to schools, parents and pupils and the wider public."
In a government consultation exercise six out of 10 respondents seemed to be in favour of KS3 league tables being published.