Data released under the Freedom of Information Act shows that the regulator opened 15 complaint cases about the RSPCA in 2016, some way ahead of the next two charities on the list, the National Trust and the Royal British Legion, both on seven complaint cases.
Macmillan Cancer Support and the Canal & River Trust were next on the list, with six complaint cases each, and the British Heart Foundation, Cancer Research UK and a charity responsible for running a recreation ground in Swanley, Kent, were the subject of five complaint cases.
The commission said it opened four complaint cases into a further 11 charities but did not name them in its response.
The RSPCA came top of the same list in 2015, with 17 complaint cases opened.
The regulator’s latest response, from Lucy Breakspere, complaints and freedom of information manager at the commission, included a number of caveats, such as that it does not maintain a definitive list of all the complaints it receives.
Breakspere said, for example, that the list did not include formal inquiries, complaints made over the telephone that were resolved during the call and complaints received about charities dealt with in the context of cases that were primarily about other issues, such as considering a land transaction.
She also pointed out that the number of complaints received about a charity did not necessarily imply any wrongdoing by the charity.
"For example, if a charity has taken a well-considered but unpopular decision, this might result in complaints but does not mean that the trustees have acted improperly," she said.
The charities respond
A spokeswoman for the RSPCA said: "The RSPCA receives more than one million calls for help and investigates more than 150,000 complaints of alleged cruelty every year. Given the highly emotive and complex nature of our work, there will inevitably be some people who are dissatisfied.
"Although we are never complacent and regard any complaint as one too many, the 15 complaints amount to 0.1 per cent of the alleged cruelty investigations undertaken. The RSPCA sets high standards for our staff and we are proud these are being met in the vast majority of cases."
A spokeswoman for the Royal British Legion said: "We greatly value input from our supporters and take every complaint extremely seriously. It is important that members of the public are able to voice their concerns to the Charity Commission. When they are passed to us, we will fully investigate each complaint and, where appropriate, take action to resolve them."
A spokeswoman for Macmillan said the regulator did not refer any of the complaints to the charity.
A spokeswoman for the Canal & River Trust said: "We take all complaints seriously and have a robust internal system in place, as well as an independent ombudsman, to review and respond to each one. There are about 380 million visits to our 2,000 miles of canals and rivers each year and we are committed to delivering the best possible experience to our visitors and customers."
Simon Gillespie, chief executive of the British Heart Foundation, said the charity was disappointed if anyone felt they had to complain to the regulator for any reason, but it treated the very small numbers of complaints it received very seriously. "We work closely with the Charity Commission and other regulators to respond constructively to any complaints we receive," he said.
Claire Wilson, head of supporter services and operations at Cancer Research UK, said the charity wanted to make sure that supporting its work was a positive experience for everyone and took very seriously any complaints it received.
Steve Nash, town clerk and chief executive of Swanley Town Council, which is the sole trustee of the Recreation Ground charity, said he believed the complaints were related to plans for a development on the site owned by the charity, which had since been dropped.
A spokesman for the Charity Commission said the regulator opened 1,024 cases to address concerns about charities in 2014/15.
"If we receive complaints about a charity, this does not necessarily mean the organisation has acted wrongly or contrary to its charitable purpose," he said. "Similarly, a charity might be subject to a serious compliance case or investigation and not be reflected in complaints statistics.
"We assess every complaint received against our risk framework and, where we don’t identify regulatory concerns, we will take no action."