Charity Business, a firm that provides back-office services to charities, has applied to the courts for the company to be wound up.
The firm, which offered services including payroll, accountancy and payment processing, and says on its website that it supported more than 200 not-for-profit organisations including the National Trust and Keep Britain Tidy.
In a brief email to clients, the company said: "It is with sadness that the directors of CBusiness Holdings have resolved to the shareholders that the company be wound up voluntarily."
Fiona Blacke, chief executive of the National Youth Agency, a Charity Business client, said she was worried that many of the firm’s other clients would face difficulty paying their staff or accessing their own financial information.
"We’re in a good position compared with a hundred other charities, because Charity Business provided such a bad service that we were getting ready to leave," she said. "But other organisations have outsourced all of their finance functions to Charity Business, and will have real trouble carrying out end-of-month payroll.
"I wouldn’t be surprised if some people go out of business as a result."
Charities had been told their documents were in storage and that they had 28 days to reclaim them before they were destroyed, she said.
Another charity worker, who asked not to be named, said: "Some people used Charity Business for invoicing, and those invoices now won't be paid. A lot of local Age UKs used it for payroll services, and they will have staff wondering if they have been paid.
"While people may get their paperwork back, I'd be surprised if they got their digital records. "I would advise people to cancel any direct debits to Charity Business, and remove permission for them to carry out any transactions on your behalf."
The National Trust, which was cited as a client by Charity Business, said it had only used the service once in 2006.
Charity Business could not be reached for comment.