Thousands of schools may now have to negotiate their own agreements with teachers to staff the centres, after a recommended pay rate of #163;9.72 an hour was withdrawn by Education Secretary David Blunkett.
Teaching unions had rejected the rate, saying it was too low, and that payment should be based on individual teachers' salaries.
But they are now warning that the lack of national guidance could discourage governors from bidding for a centre.
"If the funding had been upfront and available for all schools, with adequate remunerati on for teacher involvement, it would have gone very smoothly. As it is . . . the bidding system and payment of teachers is being left to individual governing bodies," said Olwyn Gunn, of the National Association of Schoolmasters Union of Women Teachers.
She added: "We regard it as essential that any teacher who agrees to participate in the development and delivery of study support should be recognised and rewarded for their efforts at a rate at least commensurate with their existing salary."
Study support is seen as a key part of the Government's standards raising agenda, and ministers want a centre in half of secondary schools and a quarter of primaries by 2003, funded by the National Lottery.
The Government's national framework document on study support acknowledged the need for schools to be able to recognise and reward teachers' participation. It endorsed a review body recommendation that teachers be paid on the extra duties allowance.
That was withdrawn, after consultations - leaving governing bodies to tackle the problem.
Mike Walker, assistant secretary of the National Employers Organisation for School Teachers, is also concerned about the potential for division between schools.
"We are concerned about what we call the disaggregation of duties and the possibility of payment for a duty which may be seen as ordinary by another teacher," he added.
"Cherry-picking things may lead to teachers not understanding why their particular activity is not favoured in the same way."
He would prefer schools to consider whether study support duties could be taken into account within existing salary structures.
But the consultations on payments assumed study support would be voluntary - in which case, teachers should be paid a rate reflecting their current salaries, say the teaching unions.
The NUT's response to the study support framework paper warns: "Involvement in study support centres must be based on the voluntary decision of each teacher. . . proper consultation should take place on the rate of pay for separate posts in study centres."