Flavour changing (FC) neutrino-matter interactions have been proposed as a solution to the atmospheric neutrino anomaly. Here we perform the analysis of the full set of the recent 52 kTy SUPER-KAMIOKANDE atmospheric neutrino data, including the zenith angle distribution of the contained events as well as the higher energy upward-going stopping and through-going muon events. Our results show that the FC mechanism can describe the full data sample with a χ²_min = 44/33 d.o.f. which is acceptable only at the 90.5 confidence level, while the ν_μν_τ oscillation scenario gives a χ²_min = 23.5/33 d.o.f. which is valid at the 11 CL. The combined analysis confines the amount of FC to be either close to maximal or to the level of about (10-50).