Galaga was originally conceived as a way to utilize Galaxian's PCB boards after they were overmanufactured, but while creating a partially-complete prototype, R&D engineer (and future Namco president) Shigeichi Ishimura decided that Galaga should use its own unique PCB hardware.

The iconic "Challenging Stages" from Galaga originated as a glitch discovered by programmer Tetsu Ogawa, where Galaga forces would appear and then fly off without breaking formation, with the glitch preventing them from attacking the player. As the developers were looking for bonus content in the same veins as Pac-Man's Coffee Break cutscenes or Rally-X's own Challenging Stages, it was decided this glitch could be implemented with more enemy patterns as the game's equivalent to those, and would add more replay value.