Musgraves, owners of the Supervalu and Centra brands, have said any of their stores selling pay-as-you-go electricity and gas, display notices stating they charge fees for the service.
Retailers say they have been making losses on the top-up transactions.
This follows the revelation by the Money Advice and Budgeting Service that virtually all shops in a socially deprived Dublin suburb are imposing a surcharge of as much as 10% on the service that was set up to help households reduce arrears on utility bills.
At least 150,000 households top up energy cards several times a month, mostly in a Government-backed push to reduce the rate of disconnections.
An agreed percentage of each transaction goes towards reducing arrears.
Electric Ireland promises it will not cost more than the standard rate.
However, in May MABS found that seven out of nine shops in a Dublin suburb were imposing a 20 to 50 cent surcharge on each transaction.
In spite of MABS' protests, the surcharging was continuing late last month.
Airtricity described it as a "completely unacceptable practice" by "a small minority of retailers" while Electric Ireland and Bord Gáis Energy expressed strong opposition.
BWG Foods said it has been made aware of concerns of its independent retailers - Spar, Eurospar, Mace, Xpress Stop and XL - in relation to providing energy top services.
It said many retailers have seen a significant increase in the volume of transactions over the past 12 months and have said the fee agreed with the service provider does not in all cases cover the cost to the retailer.
BWG Foods said it is aware that a small number of retailers are implementing a surcharge, but "at no point has the company instructed its retailers in this regard".
The company said it has raised the issue with the service providers and talks are ongoing on agreeing "a more fair and equitable" return for providing the service.
RGDATA has called on the utility companies to properly reimburse retailers for providing pay-as-you-go services in local shops.
The representative association said service providers have said that utility companies have consistently said they are not prepared to increase payments to retailers to cover the cost of providing the service.
PayPoint, one of the companies providing the pay-as-you-go service at retail shops, has said surcharging customers for cash transactions contravenes the contract retailers have signed with it and has already resulted in one shop being dropped from the scheme.
PayPoint claims the breach of contract occurs whether or not the retailer gives notice to customers beforehand.
It said it is also in the process of serving notice on other surcharging retailers.
The British-based electronic payments company said the situation has arisen because banks have recently increased charges for depositing cash by as much as 100%, which is having what it describes as "a devastating impact" on all small businesses including retailers.
PayPoint said it has been urgently exploring ways of helping its 320 or so retail partners to avoid having to make payments directly into banks and will make an announcement at the appropriate time if the initiatives are successful.