Beatrice Kirn, head of the association which serves two cantons around the Swiss city of Basel, told AFP it received an envelope containing 50 1,000-franc notes in the mail.
Along with the cash was a card saying simply "donation for the new centre."
The local Basler Zeitung newspaper had reported Sunday that the agency needed some 10.5 million francs to build the new visitors' centre.
"We had already received four million francs in donations, and we had two million saved, but we're still 4.5 million francs short," Kirn said.
The 1,000 Swiss franc note is the second most valuable bank note recognised as tender around the world, worth $1,056.
Singapore's $10,000 bill, worth just over $7,800, is primarily used for bank-to-bank transactions, although it is legal tender.