Structural properties of rare earth niobates (RE3NbO7, RE=Y, Er, Yb, Lu) have been studied using selected area electron diffraction (SAED) and high resolution transmission electron microscopy (HRTEM). SAED patterns show diffuse scattering features along the [111] direction of the pure fluorite (Fm3m) structure due to a short-range ordering of anion vacancies in the fluorite structure or the change of coordination number around some cations. The latter is related to the presence of small domains of pyrochlore phase (Fd-3m), which are observed in the HRTEM images.