We study the dynamics of a nanomechanical resonator (NMR) subject to a measurement by a low transparency quantum point contact (QPC) or tunnel junction in the non-Markovian domain. We derive the non-Markovian number-resolved (conditional) and unconditional master equations valid to second order in the tunneling Hamiltonian without making the rotating-wave approximation and the Markovian approximation, generally made for systems in quantum optics. Our non-Markovian master equation reduces, in appropriate limits, to various Markovi