GCSE and vocational results showed the greatest improvement for more than 10 years in 2005 - but the rise was overshadowed by controversy over the accuracy and credibility of league tables.
Local authorities have reacted furiously after the Government published council-by-council data, despite serious problems with it.
Results for 46 of the 150 councils in England were released with a note suggesting their scores were more than a percentage point lower than they should have been, after vocational results were released late by awarding bodies.
The TES understands the problem was a late release of general national vocational qualification results by the Edexcel board.
A spokeswoman for the board said problems arose because some schools had not got in touch to tell them they wanted to accept their GNVQ results as the final marks.
Schools could opt to re-sit elements of the qualifiction, she said, which meant that results data would not be complete until the school had accepted the marks.
Wandsworth, in south London, expects its final figure for the proportion of pupils getting five C grades or better to be 54 per cent, three points higher than the published figure of 51 per cent.
Paul Robinson, director of education, said he was bemused that ministers had not held up publication of results until they had accurate figures.
Overall, the percentage of pupils in England achieving five Cs or better at GCSE or vocational equivalent rose from 53.7 to 55.7 per cent.
The rise meant ministers hit their improvement target for the year, and suggests the Government may be on course to achieve its goal of 60 per cent by 2008.
Ruth Kelly, Education Secretary, said it was a "tremendous achievement".
The improvements are being driven partly by GNVQ results. The proportion achieving five Cs or better at GCSE alone rose from 50.2 to 51 per cent this year. It has improved by one point since 2002.
Provisional figures suggested England's top-performing local authority is Trafford, with 70 per cent of 15-year-olds achieving five good grades. The most improved was Stockton-on-Tees, whose figure rose 9 percentage points to 55 per cent.
A BBC study revealed last week that of nearly 2,000 secondaries whose headline results improved from 2001-4, one in six registered falls in the number of pupils achieving five or more C-grade GCSEs including English and maths.
Some of England's most improved schools on the Government's official measure had less impressive figures when English and maths were included, the research showed.