We consider a modified dispersion relation and its effect on the flavour ratios of high-energy neutrinos originated at distant astrophysical sources such as active galactic nuclei. This dispersion relation arise naturally in different new physics (NP) effects such as violation of CPT invariance, of the equivalence principle and of Lorentz invariance. It is a common notion in the literature that by using the flux of high-energy neutrinos expected from distant astrophysical sources, the sensitivity to possible NP effects may be improved beyond the current bounds. However, performing a realistic analysis that takes into account the expected number of events in future neutrino telescopes, we find that the average detected flavour ratios with and without the inclusion of new physics have essentially the same value, making difficult to obtain an improved bound for this type of new physics. © 2008 American Institute of Physics.