The reduction in neutralisation efficiency of positive ion beams compared to theoretical calculations has been acknowledged for some time. The effect has been ascribed to a depletion of the gas target in the neutraliser, although the cause of this has been the subject of debate. Recent measurements in the neutraliser of the JET Neutral Beam Injection system showed a significant increase of the gas temperature, supporting the gas heating hypothesis. This work presents direct measurement, by two methods, of the power contained in the neutral component of the JET neutral beam injection system that confirms the neutralisation shortfall. A calorimetric technique is used to compare the power within the full (i.e. ions and neutrals) and neutral beam components for the high current JET triode injectors, from which the effective gas target can be derived. The results of these measurements are confirmed by considering the response to neutral beam injection of the energy stored in the tokamak plasma. Finally, the gas heating model, combined with earlier measurements of the gas temperature in the neutraliser, is used to support the hypothesis that the target depletion is due to indirect heating of the neutraliser gas by the beam.