The contribution is devoted to formulate an averaged mathematical model describing the dynamic behaviour of the composite annular plates resting on elastic heterogeneous foundation with two foundation modules. The plates are made of two-phased, functionally graded — type composites. In contrast to most of the papers in which material properties vary through the plate thickness, in the presented study we have dealt with the plate and foundation in which effective properties vary in a radial direction of the plate. The formulation of the macroscopic mathematical model for the analysis of the dynamic behaviour of these plates will be based on the tolerance averaging technique (Woźniak, Michalak, Jędrysiak, [ed]). This averaging method is an alternative to known asymptotic homogenization. The general results of the contribution will be illustrated by the analysis of free vibrations of the composite plates on heterogeneous foundation. The results obtained from the tolerance model were compared with the results obtained from FEM. There were compared the first four natural frequencies. A good consistency of the results from both methods was obtained.