Vortex lattices in rapidly rotating Bose–Einstein condensates are systems of topological excitations that arrange themselves into periodic patterns. Here we show how phase-imprinting techniques can be used to create a controllable number of defects in these lattices and examine the resulting dynamics. Even though we describe our system using the mean-field Gross-Pitaevskii theory, the full range of many particle effects among the vortices can be studied. In particular we find the existence of localized vacancies that are quasi-stable over long periods of time, and characterize the effects on the background lattice through use of the orientational correlation function, and Delaunay triangulation.