The charity, which asked not to be named, had booked and paid for a legitimate quarter-page advert in Third Sector.
It was later contacted by a female employee from Business UK, who offered to upgrade the ad to a half-page at a reduced price. She said it would not have to pay the amount originally agreed with Third Sector.
A spokeswoman for the charity said that it eventually agreed to the offer because the saleswoman was "very persuasive and convincing".
The charity did not realise anything was wrong until it received an invoice from Haymarket, the company that publishes Third Sector, for its advert.
Martin Scott, a director at Business UK, said he thought the employee concerned had left the company. "It must be a misunderstanding," he said.