Relatives have been fighting for years to give their loved ones a burial under their own names and near their families.
"Spanish democracy is finally providing answers for these victims," government spokesperson Isabel Rodriguez said on state-owned TV station 24H.
The process of identifying the remains could take weeks or months, meaning the results will probably be published after the election.
Spain transitioned to democracy following Franco's death in 1975.
Reporting by Inti Landauro; editing by Charlie Devereux and Angus MacSwanOur Standards: The Thomson Reuters Trust Principles.
Persons:
Read, General Francisco Franco, Franco, Pedro Sanchez, Isabel Rodriguez, Sanchez, Jose Antonio Primo de Rivera, Inti Landauro, Charlie Devereux, Angus MacSwan
Organizations:
Socialist, People's Party, Falange, Association, Twitter, Thomson
Locations:
Cuelgamuros, Madrid, Spain, MADRID, Spanish