Swift heavy ions (SHI) with electronic energy loss exceeding a value of 14.4 keV nm−1 create amorphized latent tracks in YBCO type superconductors. In the low fluence regime of an ion beam where tracks do not overlap, a decrease of the superconducting transition temperature as probed through resistivity studies, is not expected due to availability of percolating current paths. The present study however shows Tc decrease by about 1–3 K in thin films of YBCO when irradiated by 250 MeV Ag ions at 79 K at a fluence of 5 × 10^10–1 × 10^12 ions cm−2. The highest fluence used in the present study is three times less than the fluence where track overlapping becomes significant. The Tc tends to increase towards the preirradiation value on annealing the films at room temperature. To explain this unusual result, we consider the effect of ion irradiation in inducing materials modification not only through creation of amorphized latent tracks along the ion path, but also through creation of atomic disorder in the oxygen sublattice in the Cu–O chains of YBCO by the secondary electrons. These electrons are emitted radially from the tracks during the passage of the SHI. Considering the correlation between the charge state of copper and its oxygen coordination, we show in particular that the latter process is a consequence of the inelastic interaction of the SHI induced low-energy secondary electrons with the YBCO lattice, which result in chain oxygen disorder and Tc decrease.