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We show that the detailed atomic structure of vacancy complexes in Si can be experimentally determined by combining positron lifetime and electron momentum distribution measurements. The divacancies, vacancy–oxygen complexes (A-centres) and vacancies paired with a donor impurity, V–P and V–As (E-centres), are identified in electron-irradiated Si. The formation of native vacancy defects is observed in highly As-doped Si at the doping level of 1020 cm−3. The defects are identified as monovacancies surrounded by three As atoms. We verify the formation mechanism of these defects by annealing experiments in irradiated Si. We show that the migration of V–As pairs at 450 K leads to the formation of V–As2 complexes, which convert to V–As3 defects at 700 K. These results explain the electrical deactivation and clustering of As in epitaxial or ion-implanted Si during postgrowth heat treatment at 700 K.