Mexico City prosecutors say in a statement the three men were let go after investigators found no evidence linking them to the May 26 disappearances.
Prosecutors said Monday that four other suspects remain in custody. They include Ernesto Espinoza Lobo, who is the co-owner of the after-hours bar from which the group was abducted.
Police in Morelos state this month found the charred body of another co-owner, Dax Rodriguez Ledezma.
Prosecutors have said the abductions were linked to a dispute between two rival drug gangs in Mexico City's rough Tepito neighborhood.