New value-added measures being piloted by the Welsh Assembly could underestimate the performance of schools with a high proportion of special-needs pupils.
Only one of the methods takes account of special educational needs - an omission described as surprising by a government expert.
Professor David Reynolds, who lives in Wales and is a member of the Department for Education and Skills's value-added advisory group, said value-added measures were essential to help identify and learn from "truly good" schools, rather than those with good catchment areas.
But he added: "If you are not using SEN, schools with special units or a high proportion of SEN pupils may be disadvantaged because the true problems of their pupils may not be recognised.
"Previous attainment may pick up some of it, but not all."
The government has put out a tender to develop value-added indicators based on three models:
* previous attainment only;
* previous attainment, plus gender and month of birth;
* full contextual information, such as free school meals and demographic data.
It is expecting tenders to include SEN as a contextual factor under the third model, and to provide clear evidence of SEN's relevance to educational attainment.
LEAs in Wales have been buying a value-added package from the Fischer Family Trust for several years, and in 2004 the Assembly bought school and LEA-level value-added data from the trust.
Welsh schools were sent a selection of value-added indicators in March this year, measuring key stage progress and predicting future results based on recent attainment.