The Royal Mail will not allow charities to claim refunds for the fees they are charged when donors using Freepost envelopes attach stamps that do not cover the entire cost of postage.
Some supporters making donations by post attach stamps to the Freepost envelopes to help charities save money, but some charities find that donors do not attach enough stamps.
In these cases the Royal Mail charges a 'process fee' of £1, plus the outstanding postage cost.
The African Children's Education Trust is one charity to have been caught in this way.
The organisation's chief executive, David Stables, said: "Perhaps these people think that any stamp they use on a Freepost envelope is an added extra. But it costs the charity money."
He said the charity did not ask donors to put stamps on Freepost envelopes, but about half of those who used them did so anyway.
A spokesman for Royal Mail said that charities should encourage their supporters either to use the correct postage or to stop putting stamps on the Freepost envelopes that they provide.
"We have to treat every customer in the same way," he said. "We can't give charities special treatment."
The majority of customers did not get normal postage costs wrong, the spokesman added.