We have studied the consequences of breaking the CPT symmetry in the neutrino sector, using the expected high-energy neutrino flux from distant cosmological sources such as active galaxies. For this purpose we have assumed three different hypotheses for the neutrino production model, characterised by the flavour fluxes at production phi(0)(e) : phi(0)(mu) : phi(0)(tau) = 1 : 2 : 0, 0 : 1 : 0, and 1 : 0 : 0, and studied the theoretical and experimental expectations for the muon-neutrino flux at Earth, phi(mu), and for the flavour ratios at Earth, R = phi(mu)/phi(e) and S = phi(tau)/phi(mu). CPT violation (CPTV) has been implemented by adding an energy-independent term to the standard neutrino oscillation Hamiltonian. This introduces three new mixing angles, two new eigenvalues and three new phases, all of which have currently unknown values. We have varied the new mixing angles and eigenvalues within certain bounds, together with the parameters associated to pure standard oscillations. Our results indicate that, for the models 1 : 2 : 0 and 0 : 1 : 0, it might be possible to find large deviations of phi(mu), R, and S between the cases without and with CPTV, provided the CPTV eigenvalues lie within 10(-29) - 10(-27) GeV, or above. Moreover, if CPTV exists, there are certain values of R and S that can be accounted for by up to three production models. If no CPTV were observed, we could set limits on the CPTV eigenvalues of the same order. Detection prospects calculated using IceCube suggest that for the models 1 : 2 : 0 and 0 : 1 : 0, the modifications due to CPTV are larger and more clearly separable from the standard-oscillations predictions. We conclude that IceCube is potentially able to detect CPTV but that, depending on the values of the CPTV parameters, there could be a mis-determination of the neutrino production model.