Tests for children who failed to reach the expected level at primary school were at the heart of the Government's strategy to overhaul secondary education.
Thousands of 12-year-olds sat the national tests in English and maths last May - taking the same papers as 600,000 11-year-olds.
However, as The TES revealed last year, most of the pupils who took the tests in the 200 pilot schools still failed to reach level 4.
Doubts were raised about the effectiveness of summer schools and catch-up classes run by schools to bring children up to scratch. The tests were also condemned for setting pupils up to fail.
Now the Government has admitted that it was a mistake to use the 11-year-olds' paper. It has asked the Qualifications and Curriculum Authority to introduce new tests that reflect what borderline children have actually been taught in their first secondary year.
The alternative papers will be piloted by some schools this year. However, other secondaries are still being encouraged to put 12-year-olds through KS2 national tests.
The move comes as English teachers across the country have been told to drop another set of tests for 12 and 13-year-olds.
The National Association for the Teaching of English has written to heads of departments advising them to avoid the tests - which teachers must mark themselves - despite ministers' claim that they are a vital measure of progress.
Anne Barnes, a NATE committee chair, said: "There is a real danger that optional tests will dominate and narrow the curriculum. In their present form they do not seem at all useful."
Meanwhile, special schools are angry that ministers have decided money for booster classes will not go to them.
Secondary schools will receive pound;4,500 this month to run the classes for Year 9 pupils in a bid to improve key stage 4 results, but special schools and pupil-referral units will miss out.
Geoff Price, head of Warwick Road special school in Bishop Auckland, said it was proof that the Government had no regard for the progress of special needs pupils whose scores might not count towards targets.
A Department for Education and Skills spokeswoman said: "Booster funding is targeted at pupils who are borderline level 4level 5 in Year 9. This is constantly under review."
She added that special schools and referral units already gave intensive support to pupils.