A process for activating Mg and its relationship with vacancy-type defects in Mg-implanted GaN were studied by positron annihilation spectroscopy. Mg+ ions were implanted with an energy of 10 keV, and the Mg concentration in the subsurface region (≤ 50 nm) was on the order of 1019 cm−3. After the Mg-implantation, N+ ions were implanted to provide a 300-nm-deep box profile with a N concentration of 6 × 1018 cm−3. From capacitance–voltage measurements, the sequential implantation of N was found to enhance the activation of Mg. For N-implanted GaN before annealing, the major defect species were determined to Ga-vacancy related defects such as divacancy. After annealing below 1000 °C, the clustering of vacancies was observed. Above 1200 °C annealing, however, the size of the vacancies started to decrease, which was due to recombinations of vacancy clusters and excess N atoms in the damaged region. The suppression of vacancy clustering by sequential N-implantation in Mg-implanted GaN was attributed to the origin of the enhancement of the Mg activation.