The tables will also be the first to take into account the impact of newly-arrived refugee children.
Other changes include details of a pilot project measuring the value-added by schools to the performance of pupils between 16 and 18, and more information on the proportion of pupils in each school with special needs.
In the longer term, considerable changes are expected to the post-16 tables as GNVQs are replaced by vocational A-levels.
Department for Education and Employment officials say the tables have been adjusted to ensure candidates permanently excluded in the past two years are added back into their excluding schools' data "as a penalty".
Schools which have accepted such pupils will benefit twice, by being given credit for any examination success they achieve, but not having them included in their examination cohort group.
John Dunford, general secretary of the Secondary Heads' Association, has written to schools minister Jacqui Smith to protest at the move, which he says is contrary to the Government's recent relaxation of retrictions on schools' rights to exclude difficult pupils.
But DFEE officials say ministers are keen to ensure excluded pupils do not miss out on the opportunity of sitting exams. They say 1,546 schools, which between them have excluded 3,006 pupils, will lose out from the adjustment. Only 306 schools which have admitted 371 excluded pupils will benefit - leaving 2,635 15-year-olds unaccounted for.
Some of the teenagers will be in pupil referral units, further education, or receiving home tuition.
Far fewer schools and pupils are affected by the concession on refugee children. In the secondary sector, 274 schools asked for the results of 1,216 pupils to be removed from their performance data, while 654 primaries asked for adjustments for 1,281 pupils.
Both the exclusions and refugee adjustments will be included in results at education authority level, but not the national figures - against which Education Secretary David Blunkett's performance is being judged.
New vocational qualifications which ministers hope will provide a high-status job-related alternative to GCSE will fail unless they do more than relaunch existing courses, warn educationists.