A vector integral–differential equation to describe electromagnetic wave propagation in nanowaveguides and photonic crystals containing thin metal layers is developed. Exact solution of the equation is obtained with the Galerkin method, taking into account the complex dielectric permittivity of metals in the optical range. A simple method for finding complex effective refractive indices for low-loss waveguide structures is developed and proved. Surface plasmon-polariton waves are simulated in the structures under consideration.