To clarify the existence of cation vacancies in Ce-doped Gd3Al2Ga3O12 (Ce:GAGG) scintillators, we performed gamma-ray-induced positron annihilation lifetime spectroscopy (GiPALS). GiPALS spectra of GAGG and Ce:GAGG comprised two exponential decay components due to positron annihilation at bulk and defect states. By an analogy with Ce:Y3Al5O12, the defect-related component was attributed to Al/Ga–O divacancy complexes. This component was weaker for Ce,Mg:GAGG, which correlated with the suppression of electron traps responsible for phosphorescence. O vacancies were charge compensators for Al/Ga vacancies. The lifetime of the defect-related component was changed by Mg co-doping. This was explained by the formation of vacancy clusters.