Context. In preparation for the COROT mission, an exhaustive photometric study of Be stars located in the seismology fields of the mission has been performed. The very precise and long-time-spanned photometric observations gathered by the COROT satellite will give important clues on the origin of the Be phenomenon. Aims. The aim of this work is to find short-period variable Be stars located in the seismology fields of COROT, and to study and characterise their pulsational properties. Methods. Light curves obtained at the Observatorio de Sierra Nevada, together with data from Hipparcos and ASAS-3 for a total of 84 Be stars, were analysed in order to search for short-term variations. We applied standard Fourier techniques and non-linear least-square fitting to the time series. Results. We found 7 multiperiodic, 21 mono-periodic and 26 non-variable Be stars. Short-term variability was detected in 74% of early-type Be stars and in 31% of mid- to late-type Be stars. We show that non-radial pulsations are more frequent among Be stars than in slow-rotating B stars of the same spectral range.