"The coin was stolen last night, it's gone," museum spokesperson Markus Farr said.
Given the high purity of the gold used in the coin, its material value is estimated to be $4 million.
The museum said on its website that the coin was issued by the Royal Canadian Mint in 2007 and that it was featured in the Guinness Book of Records for its "unmatched" degree of purity.
The coin, with a diameter of 53 centimetres and three centimetres thick, was loaned to the Bode Museum in December 2010.
Police said it was probably stolen by a group of thieves who entered the museum undetected through a window, possibly with the help of a ladder.
"The coin was secured with bullet-proof glass inside the building. That much I can say," Wenzel added.
"Neither I nor the Bode Museum can go into detail regarding personnel inside the building, the alarm system or security installations."
The Bode Museum has one of the world's largest coin collections with more than 540,000 items.
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