We can exclusively reveal 42 of the 88 schools involved are now withholding payments to the contract. The investigation also found:
The contract was signed in 2000 between Stoke-on-Trent City Council and a firm called Transform Schools (Stoke) Limited (TSSL). It uses multinational company Equans to maintain the facilities.
The contract is the largest of its kind in England and will be among the first PFI deals in the country to expire. After the deal ends, the private company will have no further liability.
What happens next has implications for the expiry of almost 600 similar deals covering schools and hospitals across England.
Stoke City Council said its priority was to get the schools handed over "safe, warm and dry", while the main contractor engaged under the PFI contract, Equans, said the buildings had been well maintained.