A low voltage non-volatile charge storage transistor has a nanocrystal layer for permanently storing charge until erased. A subsurface charge injector generates secondary carriers by stimulating electron-hole current flowing toward the substrate, with some carriers impacting charge in nanocrystals. The charge injector is a p-n junction diode where one polarity is source and drain electrodes and the other polarity is two split doped regions in the substrate partially overlapping the active area on opposite sides of the active area. Any misalignment of masks for making the injected doped portions is inconsequential because a misalignment on one side of the active area offsets the corresponding misalignment on the other side. The injector implanted portions with overlap in the active area always have the same total area in the active area. This leads to programming reliability.