A measurement of inclusive jet cross-sections in deep-inelastic ep scattering at HERA is presented based on data with an integrated luminosity of 21.1 pb^-1. The measurement is performed for photon virtualities Q^2 between 5 and 100 GeV^2, differentially in Q^2, in the jet transverse energy E_T, in E_T^2/Q^2 and in the pseudorapidity eta_lab. With the renormalization scale mu_R = E_T, perturbative QCD calculations in next-to-leading order (NLO) give a good description of the data in most of the phase space. Significant discrepancies are observed only for jets in the proton beam direction with E_T below 20 GeV and Q^2 below 20 GeV^2. This corresponds to the region in which NLO corrections are largest and further improvement of the calculations is thus of particular interest.