We compare the efficiency using indirect methods of boundary and near-boundary elements for building numerical-analytical solution of three-dimensional stationary heat conduction problems considering the difficult conditions heat and intensity of inner sources. We built discrete-continual model for problems with boundary conditions of the first, second and third kind using integral representations for the temperature. The computing experiments are presented to estimate errors of discretization and mathematical model approximation. Influence of the thermal flat and three-dimensional internal sources on the distribution of temperature field in the object was investigated.