We develop algorithms for energy minimization for kernels with singularities. This problem arises in different fields, most notably in the construction of space-filling sequences of points where singularity of kernels guarantees a strong repelling property between these points. Numerical algorithms are based on approximating singular kernels by non-singular ones, subsequent discretization and solving non-singular discrete problems. For approximating singular kernels, we approximate an underlying completely monotone (briefly, CM) function with singularity by a bounded CM function with controlled accuracy. Theoretical properties of the suggested approximation are studied and some numerical results are shown.