The importance of splay-thrust faults in subduction seismogenesis is increasingly acknowledged, however, their elastic interaction with the plate-interface remains unclear. Here, we use GPS velocities, constrained by millennial fault slip-rates, to study elastic fault-interactions between the plate-interface and its upper-plate splay-thrust faults from the southern Hellenic Subduction System (HSS) beneath Crete. We find that, despite its largely aseismic character, the HSS plate-interface zone is kinematically segmented, with slip-rate deficits locally reaching ~85% and ~45% of the plate convergence-rate on the western and eastern segments, respectively, and on structures different from those that ruptured historically. Although western Crete has been more active seismically during late Holocene, we find that the eastern HSS has higher seismic potential for large-magnitude (M>6) earthquakes and its interface-zone is closer to failure. Elastic fault-interactions are responsible for both significant inter-segment variability in strain-accumulation and millennial uniformity in earthquake rupture-segmentation between eastern and western HSS.