How processes inside the cell result in tissue reorganisation at the scale of the organism is a crucial question to understand embryonic development. Epithelial tissues in particular are dynamically remodelled due to forces generated in the cells, cellular rearrangements, and cell division and apoptosis. In this work, we introduce a physical description of the slow timescale behavior of an epithelium. We obtain hydrodynamic constitutive equations describing the continuum mechanics of an epithelium on spatial scales larger than a cell. Within this framework, topological rearrangements relax elastic stresses in the tissue and can be actively triggered by internal cell processes. Using segmentation of the development of the Drosophila fly wing, we analyze experimental patterns of flow field and tissue shear. We show that topological transitions respond to cell elongation with a delay, are autonomously polarised in the tissue, and can robustly control cell shape during morphogenesis.