Morrisons' customers who use the "pay at pump" services at the petrol station are being warned about pending charges.
Drivers using the supermarket's pumps need to undergo a pre-authorisation check to ensure they have enough funds to pay.
Currently Brits need to enter their card and put a PIN number in before they can fill up.
The bank then protects a sum, previously £1 but now £100, to cover the final cost.
Now since the changes, some shoppers have claimed the temporary charge has left them overdrawn for days.
One woman said she visited a Morrisons station with enough funds to cover £30 of petrol.
But the large authorisation charge led her account to show -£20 into her overdraft.
It took another two days for this to be rectified for the money to be made available again, she claimed.
Another shopper said: "I had this too and visited the store three times and it's still not back in my account five days later."
A third added: "Wow, didn't even know this, will always pay inside from now on."
Sainsbury's and Tesco shoppers faced similar issues last year.
The change has been implemented by card providers Visa and Mastercard, rather than the supermarkets.
This is because the cash is only guarded temporarily, and it cannot be used until the final accurate amount is charged.
Morrisons has advised customers about the charge to pay inside the station rather than at the pump.
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CEO of complaints and claims specialists Resolver Alex Neill urged customers to flag the issue as soon as possible.
He told the Sun: "If you find that the charge has not been released or refunded after a day or two contact your bank or credit card provider immediately, explaining what has happened.
"You should get an immediate reversal of the funds."
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