A parallel algorithm for computing the finite difference solution to the elliptic equations with non-separable variables is presented. The resultant matrix is symmetric positive definite, thus the preconditioning conjugate gradient or the chebyshev method can be applied. A differential analog to the Laplace operator is used as preconditioner. For inversion of the Laplace operator we implement a parallel version of the separation variable method, which includes the sequential FFT algorithm and the parallel solver for tridiagonal matrix equations (dichotomy algorithm). On an example of solving acoustic equations by the integral Laguerre transformation method, we show that the algorithm proposed is highly efficient for a large number of processors.