Molybdenum disulphide is a novel two-dimensional semiconductor with potential applications in electronic and optoelectronic devices. However, the nature of charge transport in back-gated devices still remains elusive as they show much lower mobility than theoretical calculations and native n-type doping. Here we report a study of transport in few-layer molybdenum disulphide, together with transmission electron microscopy and density functional theory. We provide direct evidence that sulphur vacancies exist in molybdenum disulphide, introducing localized donor states inside the bandgap. Under low carrier densities, the transport exhibits nearest-neighbour hopping at high temperatures and variable-range hopping at low temperatures, which can be well explained under Mott formalism. We suggest that the low-carrier-density transport is dominated by hopping via these localized gap states. Our study reveals the important role of short-range surface defects in tailoring the properties and device applications of molybdenum disulphide.