The organ — the biggest musical instrument in France — was not burned by the flames that destroyed the cathedral's roof and spire on April 15, 2019. But it was covered in soot and damaged by humidity.
"It is an absolute miracle that it has survived. An organ like this is enormous and looks indestructible, but it is actually very fragile," Olivier Latry, one of Notre-Dame's official organ players, told Europe 1 radio.
The mammoth task of dismantling, cleaning and re-assembling the precious instrument started Monday and is expected to last nearly four years.
Workers will dismantle its five keyboards, pedalboard and the 109 stop knobs that control airflow to its 8,000 pipes, some as high as 10 metres. The pieces will be placed in special containers inside the huge cathedral, where the cleaning and restoration will take place.
The organ, which sits under the Gothic cathedral's huge rose window, was completed in 1867, shortly after the spire, which crashed through the roof during the fire.
"We can't wait for Notre-Dame and the organ to be restored. There is some kind of magic between this instrument and the place ... it makes the stones sing," Philippe Lefebvre, another cathedral organist, told TF1 television.
President Emmanuel Macron promised after the fire to rebuild Notre-Dame within five years, a target many architects say is unrealistic.
Church officials also hope Notre-Dame will be open for Mass by 2024, when Paris is due to host the Olympic Games.
However, it has taken more than a year to clear out dangerous lead residue along with scaffolding that had been in place before the fire for a previous renovation effort. Reconstruction of the landmark has yet to begin.