The backdated charges have been axed after weeks of discussions between the National Federation of Sub-Postmasters (NFSP) and the Post Office.
"From September they will collect on a monthly basis," said NFSP assistant general secretary Marilyn Stoddart.
From this month retailers will have to pay 23p per £100 dispensed.
The cash machines were installed under an agreement in 2006 to distribute free-to-use ATMs to deprived areas. Hanco paid subpostmasters 11p per £100 dispensed, but the Post Office belatedly decided to charge retailers 23p per £100.
Ashok Pandey, who runs Sycamore Avenue PO in Johnston, Renfrewshire, said paying the ongoing cost would be difficult. "Thank heavens I don't have to pay back charges of more than £3,000, but in future I will have to pay."