Nationwide and NatWest both said they have fixed separate IT hitches which caused more financial chaos for customers this week.
The problems left nearly three-quarters of a million customers of Britain's biggest building society, Nationwide, out of pocket after debit card payments were taken from their accounts twice.
Nationwide said it has corrected the mistakes overnight and has promised to reimburse anyone who has incurred extra charges as a direct result.
In another blow to customers, NatWest, which is still rebuilding its customer reputation after a huge IT meltdown last month, saw its online service freeze for several hours yesterday, leaving customers locked out of their accounts, while some also had problems using debit cards.
Jenny Groves, divisional director for customer experience at Nationwide, said today: "We are pleased to confirm that all debit card transactions processed twice have now been successfully corrected.
"Once again we wish to apologise to those customers affected. We have waived all charges and are in the process of refunding any costs associated with our error. Please be assured that none of our customers will suffer financial loss as a result of this."
The building society said a "human error" meant that Visa debit card payments made on Tuesday were duplicated on Wednesday. A Visa spokeswoman said its systems had been working correctly.
Many of the society's customers did not realise what had happened until their cards were refused and some were left thousands of pounds out of pocket.
Nationwide, whose catchphrase is "On your side", recently benefited from a surge in activity from customers looking to switch accounts following the recent spate of banking scandals.
The blunder is a blow to a building society which has successfully marked itself out as offering something different from the big banks.
Nationwide said earlier this month that it had seen a 45% increase in people transferring their main account to the society, including branch, online and telephone applications.
A Nationwide spokeswoman said yesterday that 704,426 of the society's four million current account holders had been affected, of which fewer than 50,000 are thought to have been adversely impacted, by wrongly incurring charges or fees.
NatWest's latest problems come just weeks after its IT chaos which stopped people's accounts updating properly and prompted chief executive Stephen Hester to forgo his bonus this year.
The bank confirmed last night that following the new hitch yesterday, its online banking and debit transactions had returned to normal.
NatWest said that the latest problems were not related to last month's chaos and were caused by a "hardware failure" in one of its technology centres.
A spokesman said: "We continue to monitor the situation closely and apologise for any inconvenience caused.
"We will, of course, ensure that no customer is left out of pocket as a result."
Customers of both financial institutions have voiced their frustration over this week's problems.
Bride-to-be Helen Carter, 23, told the Daily Mail she had booked a £5,000 honeymoon to the Maldives, but when she checked her Nationwide account yesterday she found £10,000 had been taken out.
She told the newspaper she initially thought her account had been hacked into, adding: "This has sent us into the red and our mortgage payment is due tomorrow."
Another Nationwide customer, Leigh O'Riordan, told the BBC he had paid for his annual rail season ticket from Billericay in Essex to London, at a cost of £3,422, but found the payment had been taken out twice, leaving him without access to money.
One person wrote of their annoyance on NatWest's website that customers had been hit by yet more problems, saying: "Again? Seriously? Get your act together."
But another NatWest customer said they were sticking with the bank and accused Nationwide of "arrogance" in marking itself out from other financial institutions.
Kevin P, from Manchester said that NatWest were "humble at least," adding: "I had a Nationwide account just closed and I'm sticking with NatWest.
"Nationwide have shown a lot of arrogance with their recent ads and I don't like that."
Richard Lloyd, executive director of consumer body Which?, said: "This again raises wider questions about how robust banks' systems and safeguards are as consumers bear the brunt of yet another banking glitch."