The bust was transferred on Sunday "with extreme care" to its final resting place, the newly renovated Neues Museum, where it will take pride of place with its own display room, the authority said in a statement.
Nefertiti, renowned as one of history's great beauties, was the wife of Pharaoh Akhenaton, remembered for having converted his kingdom to monotheism with the worship of one sun god, Aton.
German archaeologist Ludwig Borchardt brought the figure to Berlin in 1913, a year after it was unearthed on the banks of the Nile.
But the bust has long been a source of friction between Egypt and Germany. Cairo alleges that Borchardt fraudulently spirited it out of the country and has demanded its return.
The neoclassical Neues Museum, which suffered heavy bomb damage in World War II, will reopen on October 17 after a more than decade-long, €200-million restoration by British star architect David Chipperfield.