A search for neutrino oscillations induced by Lorentz violation has been performed using 4,438 live-days of Super-Kamiokande atmospheric neutrino data. The Lorentz violation is included in addition to standard three-flavor oscillations using the non-perturbative Standard Model Extension (SME), allowing the use of the full range of neutrino path lengths, ranging from 15 to 12,800 km, and energies ranging from 100 MeV to more than 100 TeV in the search. No evidence of Lorentz violation was observed, so limits are set on the renormalizable isotropic SME coefficients in the $emu$, $mutau$, and $etau$ sectors, improving the existing limits by up to seven orders of magnitude and setting limits for the first time in the neutrino $mutau$ sector of the SME.
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