He was speaking at a student choices conference, organised by The Independent, as ministers prepare to unveil far reaching reforms of A-levels.
The Government is expected to keep the current A-level system, but insists that all sixth formers study so-called key skills. Employers increasingly demand that school leavers and graduates have well developed communications and computer skills when they start work.
Mr Higgins proposed the new league as part of a package of changes to the A-level tables, which are based on giving students points for each exam grade.
He said the current league was "nonsense". He said: "The points system is being used for purposes for which it was never designed. It's my view that all tables which are based on A-level points are totally, utterly completely and fatally flawed."
A Ucas report sent to ministers yesterday recommends replacing the system, which gives 10 points for an A and two points for an E, with an all embracing scheme bringing in work-based and academic qualifications.
The work, commissioned by the Government, has important implications for the crucial GCSE league table, which will be based on A-level style points from November.
Mr Higgins said: "There could also now be two league tables for schools and colleges; one having a schools performance in the mainstream qualifications like A-levels, GNVQs or Scottish highers, and a second showing its performance in inculcating key skills into its pupils. Schools could find themselves in a very different position on each of the two league tables."
Ministers are expected to put basic skills at the heart of sixth form education. But they are expected to turn down demands to broaden A-levels by introducing a European style baccalaureate, with pupils studying five or more subjects. The Prime Minister in particular is understood to have feared accusations of watering down the "gold standard" of A-level.
Even the idea of an optional diploma covering A-levels and vocational studies is thought to have been shelved.
At present, a small proportion of marks at A-level is allocated for grammar and spelling. Key skills will be marked separately and shown on the certificate, although students taking some subjects such as maths and English will not have to take separate tests.
Speaking at the conference, education minister Baroness Blackstone called for sixth-formers to have better careers information. She said: "We expect students to become more demanding consumers, and it's absolutely right that they should be."
Diana Warwick, chief executive of the Committee of Vice-Chancellors and Principals, said: "Meeting the Government's targets for expansion will depend on students getting value and a return on their investment in terms of their time and money."Reuse content