The commission last month opened an inquiry into the charity, set up to work with poor people in Uganda, over its "business rates relief arrangements".
The commission said it understood the charity had rented properties and kept them on standby to be used for raising charity awareness.
Anthony Peers, a trustee of Art, said in a statement that his charity was legitimately claiming rate relief on empty properties on the basis that when they were next used, they would be put to a charitable use. He said that the Rating (Empty Properties) Act 2007 states that a charity can claim 100 per cent rate relief on empty property if it appears that the next use will be "wholly or mainly" for charitable purposes.
Peers said: "On numerous occasions Art has offered to meet the Charity Commission at its London headquarters but on each occasion it has cancelled, therefore Art has not had an opportunity to explain its actions."
He said trustees of Art "have acted 100 per cent correctly and honestly regarding current rating legislation" and that the properties concerned were "intended for future charitable use by Art and numerous other African charities in a bid to raise funds and hold charity awareness events."
Peers said that Meyrick Gillis, a company that helps property owners reduce the business rates they pay on empty properties, had guaranteed that "any costs relating to non-domestic rates owed will be paid by the company on the charities' behalf" and that "funds are also in place from the company should legal representation be required".
Peers said: "Art has complied with ratings legislation as stated above and therefore should receive 100 per cent mandatory empty property relief until occupation commences, then 80 per cent while in occupation."
The commission is also looking into two other charities over business rates relief arrangements. In June, the regulator opened an inquiry into the Public Safety Charitable Trust after the High Court found that it had not met the rules for charitable occupation. The charity, which was wound up in the High Court last month, now faces a multi-million-pound bill from three local authorities
The other, the Kenya Aid Programme, has been involved in a dispute with Sheffield City Council over £1.6m of unpaid rates.
In both cases the charities have taken over the occupation of privately owned properties and claimed an 80 per cent discount in business rates.
But Peers said that both these charities were claiming rate relief on a different basis to his own organisation.
A spokeswoman for the commission said she did not want to comment on an ongoing inquiry.