Two of the region's hospitals which have overspent are to be charged a percentage of their eventual debt which could amount to more than �1m. The Queen Elizabeth Hospital in King's Lynn and the West Suffolk Hospital in Bury St Edmunds are both �11m in debt.
The 10% rate is set by the government to come out of next year's budget.
The Norfolk, Suffolk & Cambridgeshire Strategic Health Authority said the usage charge is "the cost attached to spending someone else's money".
'Contain spending'
The Queen Elizabeth Hospital, which has one of the highest patient satisfaction ratings in the region, also has one of the highest debts.
A hospital spokesman said: "Effectively what they are doing is levying an interest rate charge of 10%.
"10% is very high - the Norfolk health economy has been under-funded and this has now been understood," he added.
The rate was set by the Department of Health this year.
A spokeswoman for the SHA said: "Every NHS body has a statutory duty to contain its spending within its income.
"Any overspending by an NHS body must be offset by other NHS bodies under-spending, to ensure that the NHS in total contains spending within the amounts approved by parliament," she commented.