The Wandsworth Oasis Trading Company, which has four shops in London, raises money to pay for counselling for people who are HIV-positive. It has an application for charitable status pending.
The commission investigated its links with the similarly named registered charity Wandsworth Oasis Aids Support Centre, which has not submitted any accounts since March 2005, when its income was just over £800.
Patrick Lethaby, secretary of the trading company, told Third Sector the organisations' names were similar because the company used to give its profits to the centre.
He said: "We gave it about £70,000 over three or four years, but we didn't receive any receipts or annual reports, so we stopped sending the money. Now we give to a range of charities, such as the Salvation Army and the Children With Aids Charity."
Lethaby admitted that 2007/08, when the company made charitable donations of less than £8,000 from an income of nearly £300,000, had been a poor year.
"Expenses went up, sales went down and we had staff problems," he said. "But if you look at previous years, we gave more than £20,000 a year. And with the credit crunch, we need to keep reserves."
David Moir, head of policy and public affairs at the Association of Charity Shops, said that, on average, charity shops gave 20 per cent of their annual takings to charity.
Nobody at Wandsworth Oasis Aids Support Centre was available for comment as Third Sector went to press.