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Abstract In the current epoch of neutrino physics, many experiments are aiming for precision measurements of oscillation parameters. Thus, various new physics scenarios which alter the neutrino oscillation probabilities in matter deserve careful investigation. In this context, we study the effect of a vector leptoquark which induces non-standard neutrino interactions (NSI) that modify the oscillation probabilities of neutrinos in matter. We show that such interactions provide a relatively large value of NSI parameter $$\varepsilon _{e \mu }$$ ε e μ . Considering this NSI parameter, we successfully explain the recent discrepancy between the observed $$\delta _{CP}$$ δ CP results of T2K and NOvA.