We present an efficient method for evaluating current-induced forces in nanoscale junctions, which naturally integrates into the non-equilibrium Green's function formalism implemented within density functional theory. This allows us to perform dynamical atomic relaxation in the presence of an electric current while also evaluating the current-voltage characteristics. The central idea consists in expressing the system energy density matrix in terms of Green's functions. In order to validate our implementation we perform a series of benchmark calculations, both at zero and finite bias. Firstly we evaluate the current-induced forces acting over an Al nanowire and compare them with previously published results for fixed geometries. Then we perform structural relaxation of the same wires under bias and determine the critical voltage at which they break. We find that, while a perfectly straight wire does not break at any of the voltages considered, a zigzag wire is more fragile and snaps at 1.4 V, with the Al atoms moving against the electron flow. The critical current density for the rupture is estimated to be 9.6×10 10 A/cm 2 , in good agreement with the experimentally measured value of 5×10 10 A/cm 2 . Finally we demonstrate the capability of our scheme to tackle the electromigration problem by studying the current-induced motion of a single Si atom covalently attached to the sidewall of a (4,4) armchair single-walled carbon nanotube. Our calculations indicate that if Si is attached along the current path, then current-induced forces can induce migration. In contrast, if the bonding site is away from the current path, then the adatom will remain stable regardless of the voltage. An analysis based on decomposing the total force into a wind and an electrostatic component, as well as on a detailed evaluation of the bond currents, shows that this remarkable electromigration phenomenon is due solely to the position-dependent wind force.