Appearing on the BBC Radio 4 consumer show You And Yours yesterday, Mandy Johnson, chief executive of the SCC, said the commission was telling charities that reported some incidents they believed to be serious to deal with the problems themselves.
The claims come after guidance released by the Charity Commission last month said too few serious incidents were being reported to the regulator, which was putting charities at risk of further harm.
Johnson said: "We have worked with many of our small charity members to submit serious incident reports to the Charity Commission. Sadly, we’ve found that when the matters relate to small charities, quite often the Charity Commission can be quite dismissive of the reports we have sent through."
She said that in one case, one of her organisation’s members had reported to the commission concerns about the charity’s chair, who was allegedly abusing their powers.
"We spent months and months collating evidence to demonstrate this to the Charity Commission," said Johnson.
"We were really disappointed when we got a response from the Charity Commission essentially saying that it was just a matter for the trustees to sort out between themselves."
In response to a question about whether these incidents were serious enough to warrant a direct response from the commission, Johnson said that issues like the one with the charity chair "can feel very serious to the charities involved" and should be considered as such by the regulator.
But she said the commission needed additional funding from the government if it was to fulfil its role as a regulator properly.
The Charity Commission has had its budget frozen at £20m until 2020 and is expected to launch a consultation on charging charities to fund the regulator in the near future.
In response to Johnson, Sarah Atkinson, director of policy and communications at the Charity Commission, told the programme that it would sometimes be appropriate for charities to deal with internal issues themselves.
"Our first response was that we did ask the trustees to sort it out themselves," she said. "Where that is not possible, and there is a risk to the charity, we can intervene."
Atkinson said failing to report fraud to the regulator, Action Fraud or the police risked similar incidents affecting other charities, but when asked by the interviewer she declined to support calls for a legal obligation on all organisations, including charities, to report fraud to the police.
"We think it is essential that charities report fraud to us, so what we have set out in our guidance is how and when to do that," she said.
"We do want to encourage charities to report to us. It’s not really up to us whether it should be a legal responsibility; what is up to us is that we are able to act on reports of fraud and tackle it.
"We recognise that small charities want and need support from the regulator to enable them to be resilient to fraud so that the money that is for charity gets to charity, and isn’t getting into the pockets of fraudsters."