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An efficient implementation of the nonequilibrium Green function method combined with the density-functional theory, using localized pseudoatomic orbitals, is presented for electronic transport calculations of a system connected with two leads under a finite bias voltage. In the implementation, accurate and efficient methods are developed especially for the evaluation of the density matrix and treatment of boundaries between the scattering region and the leads. Equilibrium and nonequilibrium contributions in the density matrix are evaluated with very high precision by a contour integration with a continued fraction representation of the Fermi-Dirac function and by a simple quadrature on the real axis with a small imaginary part, respectively. The Hartree potential is computed efficiently by a combination of the two-dimensional fast Fourier transform and a finite difference method, and the charge density near the …