Many charities supply Freepost envelopes to donors, but tell them that if they use a stamp, it will save the charities money.
However, an automated system for sorting Freepost envelopes, introduced three years ago, cannot tell whether envelopes are stamped.
So unless Royal Mail staff spot the stamps and remove the letters from the automatic system, the charity will pay postage and the donor's stamp will usually be wasted.
Charities can compare the number of stamped letters they get with their Freepost bill and claim the difference from Royal Mail. However, it is understood that few do this.
WaterAid has stopped asking donors to put a stamp on its Freepost envelopes, and Samaritans has changed its wording from "if you use a stamp it will save us money" to "it could save us money". Many charities are continuing as before.
Jon Scourse, chief executive of the Fundraising Standards Board, said. "At best, the Royal Mail can only provide a partial service in this area and reclaims will be time-consuming and costly to resource.
"Given the lack of any guarantee from the Royal Mail that affixing a stamp will save a charity money, it is not advisable to give that impression to donors."
Lindsay Boswell, chief executive of the Institute of Fundraising, said many charities were still unaware of the situation.
"Royal Mail has failed to properly communicate to charities the change in circumstances," he said.
Twelve charities from the Direct Marketers in Fundraising Group met Royal Mail in March to discuss a solution and form a plan to inform more charities, but say a follow-up meeting planned in May was cancelled by Royal Mail.
A spokeswoman from Cancer Research UK said the charity was aware of the change and reviewing how it would affect future mailings.
A source in one major UK charity said it would continue to use the system because its savings on postage had not dropped, but admitted it had not carried out a Freepost audit since 2006.
A spokesman for Royal Mail said it was not trying to make extra revenue from the situation and, as a goodwill gesture, it already refunded charities when it was clear it had received payment through both Freepost and a stamp.
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