In spite of a raft of measures intended to encourage gender equality, a gender pay gap persists. This article identifies and quantifies precisely the main causes of the pay gap between male and female permanent staff in the three segments of the public sector. We have implemented a non-parametric decomposition method (the Nopo method), which overcomes the methodological problems inherent in conventional parametric decomposition methods. This method also enables us to obtain a very precise evaluation when it is applied to an entire population. This is the case of the data used, which come from the SIASP (public service employees information system) which exhaustively covers all public sector employees. The inequalities appear to be very different between the three segments of the public sector. Although differences in the number of hours worked systematically constitute one of the two main reasons for the gender pay gap whatever the segment of the public sector, it is in the hospital sector (excluding medical staff) that this factor plays the biggest role as it explains more than half the gap. On the other hand, in the state civil service and the territorial civil service, professional segregation, i.e. the fact that men and women do different jobs, have different professions or work in different areas, at different hierarchical levels is the main reason for the gender pay gap, explaining more than half of the difference. Furthermore, in these two segments, a significant part of this segregation is vertical in the sense that it is due to the unequal access of men and women to certain categories, sectors and ranks.