Thin films of La0.6Ca0.4CoO3 were grown by pulsed laser ablation with nanosecond and femtosecond pulses. The films deposited with femtosecond pulses (248 nm, 500 fs pulse duration) exhibit a higher surface roughness and deficiency in the cobalt content compared to the films deposited with nanosecond pulses (248 nm, 20 ns pulse duration). The origin of these pronounced differences between the films grown by ns and fs ablation has been studied in detail by time-resolved optical emission spectroscopy and imaging. The plumes generated by nanosecond and femtosecond ablation were analyzed in vacuum and in a background pressure of 60 Pa of oxygen. The ns-induced plume in vacuum exhibits a spherical shape, while for femtosecond ablation the plume is more elongated along the expansion direction, but with similar velocities for ns and fs laser ablation. In the case of ablation in the background gas similar velocities of the plume species are observed for fs and ns laser ablation. The different film compositions are therefore not related to different kinetic energies and different distributions of various species in the plasma plume which has been identified as the origin of the deficiency of species for other materials.