The fund's chairman, Ian Cheshire, also said the donation was agreed "wholly" by the five trustees at the time, and "any attempt to suggest otherwise is misleading and inaccurate".
The Prince of Wales's Charitable Fund was founded in 1979 to "transform lives and build sustainable communities", and gives grants to a wide variety of projects in Britain and around the world.
Charles, 73, has faced a series of claims about the operation of his charities. Last month the Sunday Times reported he had accepted bags of cash containing £2.5 million from Sheikh Hamad bin Jassim bin Jaber Al Thani, the former prime minister of Qatar.
London police are currently investigating a separate allegation that people associated with another of the prince's charities, the Prince's Foundation, offered to help a Saudi billionaire secure honors and citizenship in return for donations. Clarence House has said Charles had no knowledge of any such offer.
- AP