Morrisons and Co-Op are urging shoppers to use cash instead of debit or credit cards due to an IT glitch.
Both supermarket chains and their payment processing provider ACI have launched an investigation.
ACI said it is working "as quickly as possible" to fix a problem affecting card payments at branches across the country.
The issues at the retailers - which both operate stores in Lancashire and Cumbria - come as the general shift towards contactless payments continues.
Long queues were seen outside some of the Co-op's shops from Sunday amid cold weather.
In some cases, customers say they have been charged twice as a result of the problem.
"We've experienced some technical difficulties with our card payments and are working hard to resolve this as quickly as possible," said a Morrisons spokeswoman.
"We are sorry for any inconvenience this may have caused."
ACI said: "The current IT issues affect card payments at Co-op and Morrisons and we are working closely with the IT teams at both partners to resolve the problem as quickly as possible.
"We apologise to shoppers for any inconvenience caused."
A Co-op spokesman said: "Our payment processing provider is working to correct an intermittent issue which has prevented a very small number of customer transactions from being processed.
"We would like to apologise for any inconvenience caused."
The issue appears to be ongoing with customers taking to social media to complain about the situation.
"I suggest you check your declined card as my partners card got declined in Morrisons last night but they actually still took the money and we got charged twice!!"
"Charged twice for my £65 shop at @Morrisons yesterday, thanks to the card machine error. Got a declined receipt, so I'm hoping I can get a refund on this, but it's hit my available balance in my bank."
Another said: " @Morrisons I’ve got a transaction problem. I was in the store yesterday and have paid for the same shop twice as there was a problem with the card machines and it’s been taken from my bank twice. Please can somebody DM me."
If you've been charged twice, get in touch with the store directly to request a refund. You'll need to show evidence of this, such as a bank statement or receipt of the transactions that did not go through. These should say 'cancelled' or ''void' on them.
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