Intercellular Ca2+ waves (ICWs) are multicellular, coordinated oscillations of Ca2+ that transverse tissues and are functionally implicated in development, regeneration, and diseases such as cancer. However, the extent that spontaneous ICWs are a regulated phenomenon controlled by cell-cell communication networks is unclear. Here we report that ICWs exhibit spatiotemporal patterns at the organ-level using a new image analysis algorithm to quantify ICW dynamics. ICWs in the Drosophila wing disc require a specific phospholipase C, Plc21C. Further, we demonstrate that the morphogen signalling pathway, Hedgehog, modulates ICW frequency uniformly in the tissue through two distinct routes and is required for non-uniform spatial patterning of ICW amplitudes. Thus, the dynamics of spontaneous ICWs are regulated by morphogenetic signalling through two orthogonal mechanisms - frequency and amplitude - and provide an organ-scale communication system for the developing wing disc.