Birmingham-based auctioneers Fellows & Sons gave back the money on Wednesday after an investigation by St James's Palace revealed the paintings were still in Charles' possession.
Fierce bidding for the watercolours at Tuesday's sale saw the guide price of £500 to £800 for each soar, with two going for £7,300 and one for £6,000.
The firm said efforts were still being made to contact the collector who put the paintings up for Tuesday's sale and to verify the letter of provenance.
In a statement, the firm said: "Following conversations with St James's Palace, we now feel certain that these paintings are probably copies of original works.
"We have therefore refunded the purchasers fully and taken the pictures off the market."
The letter stated that the paintings had been bought at a charity auction in 1990.
'Not original'
The watercolours of Sandringham, Balmoral and Ben Avon drew bids from across the world, including the United States and Canada.
A spokeswoman for the Prince of Wales said: "The paintings sold at auction are not original watercolours by the Prince of Wales.
"We are looking into the matter and are considering all options."
The Prince never sells his paintings, but has occasionally given away originals.
The Palace confirmed none of these were among the collection auctioned in Birmingham.
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