New ways of reporting results - changed this year because of the introduction of Curriculum 2000 - will disadvantage colleges that have encouraged students to be more flexible and "mix and match".
The Association of Colleges has told the Government they are being penalised for doing what the Government has exhorted them to do - bridge the divide between academic and vocational courses.
Maggie Scott, quality adviser at the Association, said: "The new league tables will be seriously flawed, and undermine everything colleges have been trying to do. Parents are unlikely to want to send their youngsters to colleges which are apparently under-performing."
The problem arises because this year is a transition between the old curriculum and Curriculum 2000, designed to offer greater choice and flexibility to 16 to 19-year-olds.
Colleges have encouraged traditional "three A-level" students to take a vocational course as well, or offered a single A-level to those pursuing a vocational choice.
But the results announced in next month's league tables will be split over two columns, where students have taken academic and vocational courses. So, for example, a single A-level success will be recorded in the AL column. When point scores are aggregated, the results will be depressed. "It just does not represent the student's whole achievement - or the college's. Putting a footnote at the end will not solve the problem," she said.
Cathy Walsh, vice-principal of Uxbridge, said they were an improving college, and in favour of benchmarking. "But we will be penalised under this new scheme by 3 to 4 points. Nor did we receive in July a letter from the Department for Education and Skills setting out the changes in the performance tables."
A spokesman for the department said: "We want to recognise fully the excellent work that colleges do, and the overwhelming majority of respondents to consultation supported this change. The main focus of this year's tables will be the combined A-level and vocational results - which is what colleges want."