The XMM-Newton survey of the Small Magellanic Cloud (SMC) was performed to study the population of X-ray sources in this neighbouring galaxy. During one of the observations, the symbiotic binary SMC3 was found at its highest X-ray luminosity observed until now. In SMC3 wind accretion from a giant donor star onto a white dwarf is believed to cause steady hydrogen burning on the white dwarf surface, making such systems candidates for supernova type Ia progenitors. It was suggested that the X-ray source is eclipsed every ~4.5 years by the companion star and its stellar wind to explain the large X-ray variability seen in ROSAT data. We use the available X-ray data to test this scenario. We present the ~20 year X-ray light curve of SMC3 and study the spectral evolution as seen with XMM-Newton/EPIC-pn to investigate possible scenarios which can reproduce the high X-ray variability. We did not find significant variations in the photo-electric absorption, as it would be expected during eclipse ingress and egress. Instead, the X-ray spectra from different intensity levels, when modelled by black-body emission, can be better explained by variations either in normalisation (by a factor of ~50) or in temperature (kT between 24 eV and 34 eV). The light curve shows maxima and minima with slow transitions between them. To explain the gradual variations in the X-ray light curve and to avoid changes in absorption by neutral gas, a predominant part of the stellar wind must be ionised by the X-ray source. Compton scattering with variable electron column density (of the order of 5 x 10^24 cm^-2) along the line of sight could then be responsible for the intensity changes. The X-ray variability of SMC3 could also be caused by temperature changes in the hydrogen burning envelope of the white dwarf, an effect which could even dominate if the stellar wind density is not sufficiently high. ; Comment: 6 pages, 3 figures, submitted to A&A