Specialist diplomas will be launched in 2008, but they have been given a "red risk" tag in Qualifications and Curriculum Authority minutes because they have a high chance of failure, its officers believe.
Ministers say the five diplomas - in IT, engineering, creative and media, health and social care, and construction - are the biggest education reforms in the world.
But there has been confusion about what they involve. At a Westminster seminar this week, teacher unions said many of their members were mystified.
Helen Hill, head of secondary education at the National Union of Teachers, said: "Are we heading for heaven or the abyss? There is a serious communication issue between the Government and teachers."
Clarissa Williams, vice president of the National Association of Head Teachers, said. "I can think of one person who could deliver health and social care -probably the only person in the South-east."
The launch year, 2008, will be intense for schools, with the arrival of the A-level extended project, as well as a revised key stage 3 curriculum.
With the international baccalaureate to be offered to all pupils by 2010 and the establishment of an A* grade at A-level, teacher unions fear that the system could be overloaded.
"We are very concerned," said Andrew Harland, chief executive of the Examination Officers' Association. If the reforms were rushed it would be "Curriculum 2000 all over again", he said, referring to Labour's flawed reforms of six years ago. Barry Sheerman, a Labour MP and chair of the Commons education select committee, has already warned that a two-tier education system could be created, with the baccalaureate creaming off brighter students while the rest take A-levels or vocational courses.
"I would hate to see what has been termed the English genius for turning diversity into hierarchy," he said.
There were also concerns that the diplomas would be "too academic" because of the high demand they placed on pupils to achieve specific skills.
"It will actually be easier to get five GCSEs than a level 1 diploma, so those students who should be doing them will be pushed away," said Jim Dobson, director of standards at the exam board Edexcel.
However, there was broad support for the aims of the diplomas, reflected in the fact that nearly all of England's 150 local education authorities have applied to take part in the pilot.
Jim Knight, the schools minister, said the change would be "challenging" but could "transform participation and attainment".
This week, the Government named its "diploma champions", who will promote the qualifications in their respective sectors: Sir Alan Jones, chairman of Toyota; Sir Mike Tomlinson, former chief inspector of schools, Deian Hopkin, vice-chancellor of London South Bank university; and Michael Arthur, vice-chancellor of Leeds university.
The first five diplomas are in IT, engineering, creative and media, health and social care, and construction.
They will be launched in a limited number of areas in 2008.
They can be studied at three levels: the lowest corresponds to GCSE grades D-G, the highest to A-level.
Each level is equivalent to about five GCSEs or three A-levels.
They cover a range of vocational skills as well as functional skills in IT and communication.
From 2010, another nine diplomas will be launched - in environment, manufacturing, beauty, business, catering, public services, sport retail, and tourism.
Diplomas will be available across England by 2013.
Government figures show that 25 per cent of young people leave education at 16.