The government says it wants to simplify what is on offer to teenagers
The government is to start scrapping qualifications in England as the new Diplomas are rolled out to all by 2013.
Applied A-levels are likely to be the first to go, along with thousands of little-used vocational qualifications.
BTecs and City and Guilds may be subsumed in Diplomas as the system is streamlined. Colleges think A-levels will go the same way.
In what the Tories say is a U-turn, ministers are dropping Tony Blair's International Baccalaureate pledge.
The changes were signalled in a green paper for consultation, Promoting achievement, valuing success: a strategy for 14-19 qualifications.
A new Joint Advisory Committee for Qualifications Approval will decide which qualifications get public funding to be offered in schools and colleges.
NEW 14-19 STRATEGY FOR ENGLAND
GCSEs and A-levels
Others reassessed by new Committee for Qualifications Approval
To be reviewed in 2013
Of the "alphabet soup" of 6,500 or so existing qualifications 65% are taken by fewer than 100 students a year, according to the Department for Children, Schools and Families.
Those with very low uptakes - such as a certificate for parking attendants - are likely to go unless there is a proven demand from students and employers.
Schools Minister Jim Knight told reporters: "Our long-term goal is that every learner in this country has an engaging and comprehensible set of options ... that equips them well for the world of work and higher education."
He said the existing system was "overly complex" and difficult for youngsters and their parents and advisers to understand.
The new strategy would be simpler. This will be essentially three-pronged: Diplomas, GCSEs and A-levels, and Apprenticeships.
The government says it is investing to ensure GCSEs and A-levels continue to be high quality and important for "many" young people.
But it says: "Diplomas will in practice duplicate the offer currently provided by Applied A-levels, and will provide a stronger learning experience".
So from 2013 Applied A-levels "will no longer be needed as part of the qualification offer in England".
It will be up to the devolved administration in Wales and Northern Ireland to decide what to do.
Applied GCSEs, on the other hand, will stay for now.
Diplomas include an optional element which ministers say can bring in "the best of existing qualifications - for example some existing vocational qualifications such as BTecs, City and Guilds awards, OCR Nationals and others".
The strategy makes clear that this could also include A-levels and AS-levels.
Exam board Edexcel, which owns the BTec brand, said it thought the strategy meant they could continue both as an integral part of the Diploma and as stand-alone qualifications.
The whole system will be reviewed in 2013, as previously promised.
Mr Knight said: "We are completely open minded about that review at this point."
The director of learning and quality at the Association of Colleges, Maggie Scott, said: "We can see the point at which A-levels, BTec Nationals and other qualifications that serve a purpose for learners might be subsumed under the Diploma umbrella. "
The strategy calls the International Baccalaureate (IB) one of "a number of other general qualifications already in use or that schools are preparing to deliver". Another would be the new Pre-U.
It says it will be for the new exams regulator, Ofqual to consider whether they meet its accreditation criteria.
If they do, the government will consider whether they "fill a gap" and therefore should continue to be funded.
"Where we do continue to fund them, we shall include consideration of their future alongside GCSEs and A-levels as part of the 2013 review," the strategy says.
Late in 2006 the government said it would fund every local authority to have at least one centre offering the International Baccalaureate (IB) Diploma.
It now says it will not force this on the minority that have not come forward.
Shadow children's secretary Michael Gove called this a U-turn "denying students choice and closing down opportunity".
Liberal Democrat spokesman David Laws said: "It should be up to schools, not central government, what qualifications ought to be offered."
The Association of School and College Leaders and the National Union of Teachers said GCSEs and A-levels should be brought within the Diploma framework.
The general secretary of the Association of Teachers and Lecturers, Mary Bousted, said: "There is still a long way to go before we have a unified qualification framework rather than three distinct tracks - academic, occupational and vocational."