The aim of this paper is to develop an adequate mathematical model, methods and algorithms for solving three-dimensional problems for axisymmetric spatial inhomogeneous viscoelastic systems (shells, foundations and bases) and to assess the dynamics of protective shell (containment) of a nuclear power plant (NPP) under resonant modes of vibration. The problem is solved using the semi-analytical finite element method. Firstly, the eigenmodes of vibration of the system are determined in an elastic three-dimensional statement, secondly, the solution to the problem of forced vibrations of viscoelastic systems is constructed using the expansion of these eigenmodes of vibration. Viscoelastic properties of the material are described using the hereditary Boltzmann-Volterra theory. The principle of virtual displacements is used to simulate dynamic processes in inhomogeneous viscoelastic systems. The convergence and accuracy of the solutions obtained are investigated by test problems. The frequency response characteristics (FRC) in various points of the NPP containment are estimated at various viscosity parameters of the material. It was revealed that the highest amplitude of vibrations in resonance modes occurs at close values of the frequency of external effect to the first eigen frequencies of the system; in the presence of dense spectra of eigen frequencies of the system, the highest amplitudes can occur at higher frequencies of external effect.