The bill, which includes backdated equal pay claims across councils in England and Wales, could reach more than pound;3 billion. Almost a third of the workers who could be affected work in schools.
Around 270 councils have not completed the job evaluations to ensure fair pay for the most poorly paid female workers such as dinner ladies and admin staff. Although the situation varies from council to council, schools in some areas are being expected to pay their share.
In Sandwell, around 120 schools have been told they will have to pick up a pound;55 million bill if negotiations with unions fail to reach a compromise deal for all school workers eligible for back pay.
The council has offered to borrow money on schools' behalf which they can repay over five to ten years, with interest.
Two special schools, which employ a high number of support staff, could end up paying out pound;2 million each.
One Sandwell head said it was unfair to be dumped with the bill, as the amount of back pay due was inflated by the council's delay in carrying out the job re-evaluations.
Even discounting interest payments, a pound;300,000 loan on a pound;1 million school budget could cost between two and three per cent of the school budget for 10 years.
"There is a complete sense of disbelief among heads," he said. "This could make schools very vulnerable and damage children's education," he said.
Kerry George, senior assistant secretary for salaries, pensions and conditions at the National Association of Head Teachers, said schools were willing to work with local authorities, but it was "unacceptable" for schools to be threatened as they had in Sandwell.
Pauline Hinton, deputy council leader, said she had been advised that schools were liable to pay, but she hoped to reach a solution through "joint working".
She said that the pound;55m figure was a "worst case scenario" and negotiations with unions were yet to begin.
In other councils, such as Staffordshire, schools were told to start preparing to fund their back pay bill several years ago, by putting one per cent of their budgets aside.
However, schools may find this money is taken away as part of the Government's plan to "claw back" surplus budgets.
Richard Stokoe, a spokesman for Local Government Employers, said he doubted schools would be burdened with a single up-front payment for equal pay claims.
In September, the Government gave councils permission to borrow pound;500m on their own assets to help with the back pay bill.