Egypt's authorities are hoping that the new museum, which opens fully this month, will help revitalise tourism - a prime source of foreign currency for the country.
The industry has been battered by political turbulence over the past decade, and more recently by the pandemic.
Saturday's move of the mummies will be streamed online for all enthusiasts of ancient Egypt to watch.
The new exhibits will now be housed in the Royal Hall of Mummies and will go on display to the general public from 18 April.
The hall has been designed so that visitors will experience the illusion of being in the Valley of the Kings in Luxor.
Separately, a new Grand Egyptian Museum which will house the famous Tutankhamun collection is due to open next year, close to the Great Pyramids at Giza.