Research from the regulator shows that more than two-thirds of charities have no complaints procedures - and that nearly 80 per cent don't believe they need them.
"Charities without complaints procedures are missing a trick," said Rosie Chapman, executive director for policy and effectiveness at the commission.
"This is a key way for charities to make sure their services are responsive to users."
The commission's report, Cause for Complaint, says nine out of 10 charities say they don't receive complaints from service users. Of those that have complaints systems, 93 per cent have used them fewer than five times in the past year.
David Allen, chair of the Charities Complaints Forum - comprising officials from charities that do have complaints procedures in place - said this did not necessarily mean service users don't have complaints.
"Have charities done enough to make their beneficiaries aware of what they can do to complain?" he said. "Is it well publicised on their websites?"
Allen said charities should view complaints as a chance to improve services, especially in organisations that are engaged in public service delivery.
"It's more than just complaints; it's about feedback," he said.
Children's charity NCH has a three-stage procedure that uses an outside investigator if necessary. Chief executive Clare Tickell said: "It's in keeping with other sectors. If you're unhappy with local government, say, you can express concern."
Charities will have the chance to challenge the commission at the next meeting of the Charity Complaints Forum on 16 June.