Branches with cash machines introduced following the 2006 agreement to put free machines in deprived areas have received notification that they will now have to pay two years' worth of charges to the Post Office.
Mel Garbutt in Hainton, Lincolnshire, was told he would have to pay 20p plus VAT for every £100 dispensed by the ATM since April 2007, costing him several hundred pounds.
"They never said anything about these charges when I first installed the machine and why has it taken two years to ask for the money?" he said.
"If they're going to start charging I'll get rid of the machine as soon as possible. If I had been told there were going to be charges I wouldn't have had it installed," he added.
Ashok Pandey, who runs a newsagents and Post Office in Johnstone, Renfrewshire, faces charges of more than £3,200. He said that the original contract stated that machine operator Hanco would pay any charges incurred.
Hanco owner RBS said that this situation was a misunderstanding between the Post Office and subpostmasters as monthly payments have been made to subpostmasters for the use of cash supplied by Post Office Ltd in the machines.
A spokesperson for Hanco said: "We are advising all customers that if the amount being claimed by Post Office Limited is greater than the amount we have paid them to date, we will reimburse any shortfall. However, this is likely to be very few cases given that average cash withdrawal amounts are below £100."
A spokesman for the Post Office apologised for the error, but insisted that the charges would still have to be paid. He said: "Post Office Ltd is apologising to subpostmasters for having to reclaim fees for providing cash for their ATMs, for which we mistakenly did not charge. We will not be asking for these payments in a lump sum."