Concern Worldwide has charged almost 25,000 direct debit supporters up to 100 times the amount they had pledged to the charity after an administrative error.
The international poverty charity spent the weekend apologising to the 24,700 people who were affected by the blunder, which meant that regular givers who pledged £5 a month were instead charged as much as £500.
It has vowed to refund the supporters what is likely to amount to millions of pounds, as well as any bank charges or fees they incurred as a result of the unexpected withdrawal of funds.
A spokeswoman for Concern Worldwide said the charity has launched an external investigation led by the accountancy firm KPMG to find out what went wrong. She said it was not possible to say at this stage how much money was involved.
The charity initially told people it would refund them directly after the error first emerged last Friday. But on Sunday it changed its advice, saying that affected supporters would get their money back sooner if they filed an indemnity claim with their banks. They should then get an automatic refund within 48 hours, the charity said on its website.
Scores of supporters complained to the charity on Twitter. Hannah Boulton tweeted: "Absolutely not on - an admin error causing a £400 direct debit from my account? To save future issues I will no longer be donating."
Sophie Whitehead said: "Well thanks @Concern for giving me a really stressful start to the week."
Concern Worldwide has been responding to tweets with apologies and advice, as well as texting supporters and setting up a new helpline for those with concerns. Some people have complained about the "cut and paste" nature of the charity’s tweets.
"We would like to apologise unreservedly for the error and any problems this may have caused supporters," said a statement from Rose Caldwell, the charity’s UK executive director.
The charity also said on its website: "As soon as we discovered the mistake we immediately contacted our bank to try to stop them being processed but unfortunately it was too late for us to do so."
It added: "It is not an error made by the bank. We take full responsibility for the mistake."
The charity said it was the first time this had happened during the more than 10 years it has run its direct debit programme.
The environmental organisation Greenpeace experienced a similar situation in 2006, when it was obliged to reimburse thousands of supporters after a direct debit error saw donations of 100 times their normal level leave their bank accounts.
Greenpeace blamed the mistake on a combination of human error and its computer system. It said the computer key that processed the direct debits in pounds was wrongly pressed instead of the one for pence.