The energy spectrum of neutrino-induced upward-going muons in MACRO was analysed in terms of special relativity principles violating effects, keeping standard massinduced atmospheric neutrino oscillations as the dominant source of νµ ↔ ντ transitions. The data disfavour these exotic possibilities even at a sub-dominant level, and stringent 90% C.L. limits are placed on the Lorentz invariance violation parameters. These limits can also be re-interpreted as upper bounds on the parameters describing violation of the Equivalence Principle.