The aim of this paper is to analyze the role of the pressure head, i.e., the difference of total pressure forces acting on the Indonesian seas waters from the western Pacific and the eastern Indian Ocean, in driving the Indonesian Throughflow (ITF) and in determining the total transport of the ITF. These questions have been discussed in the literature but no consensus has been reached. A regional model of the Indonesian seas circulation has been developed that properly resolves all major topographic features in the region. The results of model runs have been used to calculate all components of the overall momentum balance. The estimates disclose that the dynamical balance is primarily between the volume integrated Coriolis acceleration, pressure gradient and the area integral of local wind stress. It is shown that consideration of components of momentum balance in the direction of the outflow through the Indian Ocean port leads to the formulation of a diagnostic relation between total inflow transports due to the Mindanao and New Guinea Coastal Currents and the external pressure head, internal pressure head, bottom form stress, and area integrated wind stress. Based on this relation, it is concluded that the external pressure head is not the major driving force of the ITF, which is why there is no unique relation between the total transport of the ITF and the external pressure head. However, Wyrtki's suggestion to monitor the variability of the total transport of the ITF by measurement of the sea-surface-height difference between the western Pacific and the eastern Indian Ocean is validated.