The disclosed technique for charging a battery in an implantable medical device using an external charger indirectly determines the total power dissipated as heat in the IPG (P_IPG) by accounting for the various powers in the external charger/IPG system which are either known or can be measured, such as the input power provided to the amplifier that drives the coil in the external charger (Psys), the power stored in the IPGs battery (Pstored), and the power dissipated in the external chargers charging coil as heat (P_EC) (which is measured). Determining P_IPG at the external charger in this manner allows the heat flux from the IPG to be calculated (F_IPG), and compared to a safe heat flux limit (F_IPG′) to allow for adjustment to the power of the magnetic charging field in a closed loop fashion.