Pupils permanently removed from schools up to two years ago have now been included in the GCSE cohort number despite being crossed off the school roll.
At Thurston community college, Bury St Edmunds, five pupils permanently excluded in 1998 have caused a dip in the GCSE pass rate.
When the GCSE candidate group increased from 300 to 305, the proportion of students achieving at least one GCSE fell from 98 to 94 per cent.
Annette Vaux, acting head, said: "The Government is sending mixed messages to schools by claiming to support them when they exclude pupils for a good reason but then penalising them when it comes to league tables.
"Schools that take on excluded pupils should be praised but no one makes the decision to exclude permanently lightly."
About 1,500 schools have been adversely affected by the new rule, according to the Department for Education and Employment, which has tracked excluded pupils.
Results for 306 schools who accepted xcluded pupils have been boosted. The pupils are not classed as part of the cohort group but any exam passes they achieve are included in the tables.
The move is part of the Government's drive to cut expulsions by a third by 2002, from around 12,300 to 8,000.
But the tables give no indication of which schools have been affected by the change, giving parents an unclear picture of true performance.
Schools accepting pupils newly-arrived in England have also benefited from a decision to remove those children's GCSE results.
At Moat community college, Leicester, an 18 per cent five A to C pass rate was boosted by 2 points because 21 children who have been in the school for less than two years were not included.
Headteacher Freda Hussain, said: "It is only right that schools taking in children with little or no English are not disadvantaged.
"To fit the criteria we had to show Moat was the first school these children attended. We have pupils who went to another school briefly before joining us who have to be included in GCSE results despite their equally poor knowledge of the language."