The aim of this study is to analyse the stability of the single in-plane vortex state in two-dimensional magnetic nanodots with a nonmagnetic impurity (single-spin defect) at the centre. Small square and circular dots including up to a few thousand of spins are studied by means of a microscopic theory with nearest-neighbour exchange interactions and dipolar interactions fully taken into account. We calculate the spin-wave frequencies versus the dipolar-to-exchange interaction ratio d to find the values of d for which the assumed state is stable. Transitions to other states and their dependence on d and the vortex size are investigated as well, with two types of transition found: vortex core formation for small d values (strong exchange interactions), and in-plane reorientation of spins for large d values (strong dipolar interactions). Various types of localized spin waves responsible for these transitions are identified.