Motivated by the interest in searches for violation of CPT invariance, we study its possible effects in the flavour ratios of high-energy neutrinos coming from cosmic accelerators. In particular, we focus on the effect of an energy independent new physics contribution to the neutrino flavour oscillation phase and explore whether it is observable in future detectors. Such a contribution could be related not only to CPT violation but also to a nonuniversal coupling of neutrinos to a torsion field. We conclude that this extra phase contribution only becomes observable, in the best case, at energies greater than 10^{16.5} GeV, which is about five orders of magnitude higher than the most energetic cosmological neutrinos to be detected in the near future. Therefore, if these effects are present only in the oscillation phase, they are going to be unobservable, unless a new mechanism or source capable to produce neutrinos of such energy were detected.