After The TES went to press, the Department for Education and Skills released statistics for England setting out the percentage of pupils in each local authority achieving five or more A*-C grade GCSEs or their vocational equivalent.
A national figure was also released and was expected to show an improvement on the score for 2004, which stood at 53.7 per cent.
But it is understood the figures for some authorities are lower than their true scores because of a problem the DfES has had collecting data for vocational exams.
Full results for some General National Vocational Qualifications taken by pupils have not been collected for all councils. A full intermediate GNVQ is worth four GCSEs for statistical purposes, suggesting the effect on the figures could be large.
More than 100,000 full intermediate GNVQs were taken this summer.
Many London councils believe their results are better than those published yesterday. The capital's results were expected to show the proportion of pupils achieving five or more grades at C or better rose from 51.7 to 54.2 per cent.
The national headline figure for GCSEs is also believed to be affected.
The Government's decision to allow GNVQs to count as four GCSEs for statistical purposes remains controversial amid widespread claims that the exams are not sufficiently difficult or time-consuming to justify such an equivalence.
Chris Waterman, executive director of Confed, the education directors'
association, said: "Given that the Government places such high stress on performance tables, it is incumbent on them to ensure they are accurate. If it were knowingly to publish inaccurate data, it would be unforgivable."