The central body for Jehovah’s Witnesses in Britain and a spiritual healer’s organisation were the charities about which the Charity Commission received the most complaints in the two years to March 2012.

The regulator said it had received 13 complaints about both the Watch Tower Bible and Tract Society of Britain and the NFSH Charitable Trust during the period.

The figures were revealed in response to a request under the Freedom of Information Act, made by the Conservative MP Simon Hart in July, for a list of the 10 charities about which the commission received most complaints.

The RSPCA and the JNF Charitable Trust, which is concerned with Israel, were the next most complained about, with 12 complaints to the commission over two years.

Hart, a former chief executive of the pro-hunting charity the Countryside Alliance, was one of a group of cross-party group of politicians that has called on the commission to investigate the RSPCA after it spent more than £320,000 on a successful private prosecution of the Heythrop Hunt.

The commission's list does not include complaints made to charities themselves or to other regulators such as the Advertising Standards Authority and the Fundraising Standards Board.

The commission said none of the complaints against charities in the top 10 resulted in any formal action against those organisations. It also said the number of complaints would not necessarily mean that a charity had acted wrongly or contrary to its charitable purpose.

"An internal dispute within a membership body could result in several letters of complaint or dissatisfaction, but might not be be a fair indication of the level of service that is being received by beneficiaries," said Liam Carroll, the commission’s complaints manager.

The commission received 11 complaints about both Smile Train, which provides surgery for children in developing countries with cleft lip and cleft palate, and Age UK. The National Trust and the Royal British Legion were next with nine complaints.

The Global Warming Policy Foundation and the General Medical Council made up the rest of the most complained about charities in the top 10.

It said it did not usually compile a list of most complained-about charities and had only done so in response to the FoI request.

"The number of complaints received about a charity would not necessarily mean that that charity had acted wrongly or contrary to its charitable purpose,"in his response to the request.