Due to the layered nature of graphite, the migration and interaction of point defects in the graphite crystal structure are highly anisotropic, and it is usually assumed that individual mobile lattice vacancies are confined to diffuse on a single plane. We present the results of ab initio calculations based on density functional theory which demonstrate that vacancies can, in fact, move between adjacent planes when they interact with one another via relatively low energy pathways, often with barriers of less than 1 eV. These interlayer transition mechanisms can significantly alter both the kinetics of point-defect aggregation and coalescence and also the resultant morphologies of multivacancy complexes that form as a result of migrating vacancies interacting.