The commission said it had opened an operational compliance case on the charity, which has objects including promoting the conservation, protection and improvement of the natural environment, in September 2014, when the charity reported the loss of funds.
The regulator said today that the compliance case had highlighted wider regulatory concerns, including payments made from the charity’s subsidiary company to companies linked to individuals connected with the charity, including trustees.
The commission said there were also concerns about the charity’s involvement in rate-relief schemes, which had resulted in the charity "incurring losses following legal action taken by a local authority".
It said it was also concerned that the charity had only two trustees, one fewer than the minimum number required by the charity’s governing document.
The charity had an income of £2.1m in the year to 26 June 2014 and spent £2.5m over the same period, according to its latest set of accounts on the Charity Commission’s online register.
A statement from the commission said its inquiry, which was opened on 18 June, would examine issues including the circumstances leading to the loss of funds from the alleged criminal activity and trustees’ decision-making when "entering the charity into rates-relief schemes and circumstances leading to the significant financial loss as a result of legal action taken by a local authority". It did not give any further details about the legal action.
The charity’s website shows that it arranges for social enterprises or community groups to use privately owned premises in order to secure a minimum 80 per cent reduction in business rates for its owner, in return for "sponsorship" from the landlord of 50 per cent of the costs saved on rates.
The Charity Commission said in December 2011 that it would investigate more than 700 instances in which properties might have been occupied by charities in order to claim rate relief for the landlords, rather than to use them for a charitable purpose.
The investigation came after an article in the Financial Times newspaper quoted experts who said the idea was "pushing this into the area of a scam". Healthy Planet said at the time that its dealings were legitimate.
A statement today on Healthy Planet’s website from Francesca Polini, its chief executive, said: "In September 2014 I, along with our current trustees, reported an alleged fraud and other financial irregularities to the police and to the Charity Commission.
"We are cooperating fully with the Charity Commission and the police with their respective investigations, and have ceased our relationships with all those we believe to have been involved in any wrongdoing.
"I am confident that these investigations will lead to a fair and just resolution for all involved."