It is expected that extreme mass accretion rate onto strongly magnetised neutron star results in appearance of accretion columns above stellar surface. For a distant observer, rotation of a star results in periodic variations of X-ray flux. Because the mass accretion rate fluctuates around the average value, the pulse profiles are not stable and demonstrate fluctuations as well. In the case of bright X-ray pulsars, however, pulse fluctuations are not solely attributed to variations in the mass accretion rate. They are also influenced by the variable height of the columns, which is dependent on the mass accretion rate. This study delves into the process of pulse profile formation in bright X-ray pulsars, taking into account stochastic fluctuations in the mass accretion rate, the corresponding variations in accretion column geometry and gravitational bending. Our analysis reveals that potential eclipses of accretion columns by a neutron star during their spin period should manifest specific features in pulse profile variability. Applying a novel pulse profile analysis technique, we successfully detect these features in the bright X-ray transient V0332+53 at luminosities ≳2×1038ergs−1. This detection serves as compelling evidence for the eclipse of an accretion column by a neutron star. Detection of the eclipse places constraints on the relation between neutron star mass, radius and accretion column height. Specifically, we can establish an upper limit on the accretion column height, which is crucial for refining theoretical models of extreme accretion.