Some schools will lose thousands of pounds because of changes in the funding system, according to advice given by consultant John Atkins to the National Union of Teachers.
The pledge to raise funding for every school means even the relatively well-funded will see increases - effectively locking in inequalities.
Expanding schools will receive more money than neighbours of a similar size and those with falling rolls could have budgets raided as education authorities struggle to carry out Mr Clarke's pledge. Schools' individual needs will be ignored, says Mr Atkins.
Heads waiting for money for capital work may also be disappointed as money is diverted to running costs to fulfil the Government's pledge.
Schools have shed thousands of jobs as a result of this year's funding crisis which was caused by rising costs and changes to the funding system.
Research published by the NUT last week suggests that schools face a shortfall of pound;1 billion over the next three years.
Mr Clarke announced in July that every school would be guaranteed an increase in funding per pupil as part of an pound;800 million package designed to draw a line under the crisis. But Mr Atkins warns that this could "lock in" inequalities for the future.
"The Department runs the danger of introducing a funding system where what a school received per pupil in 2003 is the single most significant determinant of its funding in the future," he said.
John Bangs, NUT head of education, said: "This is an indictment of the Government's quick-fix solution to schools' funding problems.
"The crisis will only be solved by new money not by ministers' fancy footwork."