Observations of ionised carbon at 158 micron ([CII]) from luminous star-forming galaxies at z~0 show that their ratios of [CII] to far infrared (FIR) luminosity are systematically lower than those of more modestly star-forming galaxies. In this paper, we provide a theory for the origin of this so called [CII] deficit in galaxies. Our model treats the interstellar medium as a collection of clouds with radially-stratified chemical and thermal properties, which are dictated by the clouds volume and surface densities, as well as the interstellar radiation and cosmic ray fields to which they are exposed. [CII] emission arises from the outer, HI dominated layers of clouds, and from regions where the hydrogen is H2 but the carbon is predominantly C+. In contrast, the most shielded regions of clouds are dominated by CO and produce little [CII] emission. This provides a natural mechanism to explain the observed [CII]-star formation relation: galaxies star formation rates are largely driven by the surface densities of their clouds. As this rises, so does the fraction of gas in the CO-dominated phase that produces little [CII] emission. Our model further suggests that the apparent offset in the [CII]-FIR relation for high-z sources compared to those at present epoch may arise from systematically larger gas masses at early times: a galaxy with a large gas mass can sustain a high star formation rate even with relatively modest surface density, allowing copious [CII] emission to coexist with rapid star formation.