Heads could be forced to use Gordon Brown's pound;300 million Budget windfall just to pay for the new AS-levels and key-skills qualifications, which are being introduced this September, said John Dunford, general secretary of the Secondary Heads Association.
From September, sixth-formers will take up to five subjects to AS-level in their first year, selecting around three to take on to A-level, along with a key-skills qualification. The aim is to encourage greater breadth and create all-rounders to help the country compete in the global economy.
But heads are furious that much of the pound;35m delegated to local authorities to fund the broader curriculum has not been passed on to schools. And so far only 20 universities have indicated they will give any credit to students for taking AS-levels.
Universities must also create a level playing field for applicants, Mr Dunford said, as new research revealed that students from poor backgrounds had little chance of getting into Britain's top universities - despite ministers' priority of widening access.
"When our studens apply for university, they must know what the universities' attitude is," Mr Dunford told The TES. "Will they give credit to those with four or five AS-levels or to the key-skills qualification? Will they give credit for contrasting subjects?
"If we are not absolutely clear about both funding and their acceptability to universities, then these reforms are in trouble. They could be dead in the water," he said.
Research by the Sutton Trust, which works to widen access to Britain's "Ivy League", this week showed that children from poor backgrounds had less than a one-in-100 chance of a place at one of the top 13 universities. The trust's founder, Peter Lampl, called it a "scandalous waste of talent".
SHA and the National Association of Head Teachers said universities should introduce scholastic aptitude tests - widely used in the US - which they said give a more accurate measure of students' potential than A-levels.
Half of Oxbridge places went to independent-school pupils, while just 8 per cent came from the lowest three socio-economic classes, which account for half of the population, the Sutton Trust research found.
A Department for Education and Employment spokeswoman said officials were willing to study the use of SATs in the US.