College heads have warned that the performance of their institutions will be unfairly downgraded in league tables to be published by the government next week.
The Association of Colleges says alterations to the way points are allocated will leave further education colleges on average four points below their rightful score. The tables record student achievements in A-level and vocational qualifications.
AoC leaders said that lower scores could have a "disastrous" impact on recruitment.
The changes have been introduced temporarily by the Department for Education and Skills to reflect the transition in schools and colleges from the old post-16 curriculum to Curriculum 2000, which allows students to pursue a broader range of study.
Many colleges allowed students to "dip in" to the new curriculum in the transition year by taking an A level in addition to their vocational qualifications.
The DFES has added these students to its calculations for scores in the important A-level column of its league tables, which parents and policy-makers use as a guide.
The AoC predicted that this would depress the average A-level score per student in colleges.
Maggie Scott, the AoC's curriculum and quality adviser, said: "The irony is that those colleges that have embraced Curriculum 2000 are now being heavily penalised for doing so, whereas schools that have adopted a wait-and-see approach will come out relatively well."
The DFES has said it will add footnotes to its league tables to signal the changes made.