"The burial took place overnight in the cemetery at Le Vernet, discreetly," said Bernard Bartolini, mayor of Prads-Haute-Bleone, one of the Alpine communities affected by the crash.
Up to 500 people were expected later Friday for a ceremony in honour of the victims -- which included 72 Germans and 50 Spaniards.
All 150 people on board died instantly when, according to investigators, co-pilot Andreas Lubitz deliberately crashed the flight into the mountains.
"For the families of the victims, it's a second burial because they have already buried the remains of their loved ones that could be identified by DNA," Francois Balique told AFP.
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He said there was "no other solution" than to bury the unidentified remains in a mass grave.
"It will be terrible for the families," he said.
The chief executive of Lufthansa, Carsten Spohr, will not be attending Friday's ceremony amid a spat between the airline -- the parent company of Germanwings -- and families over compensation.
The parents of 16 student victims from the town of Haltern wrote an open letter to Spohr to voice "disappointment" at Lufthansa's conduct "since a pilot from your company killed our children".