(Abridged) The Fermi/LAT collaboration recently reported the detection of starburt galaxies in the high energy gamma-ray domain, as well as radio-loud narrow-line Seyfert 1 objects. Motivated by the presence of sources close to the location of composite starburst/Seyfert 2 galaxies in the first year Fermi/LAT catalogue, we aim at studying high energy gamma-ray emission from such objects, and at disentangling the processes from starburst and active galactic nucleus activity. We analysed 1.6 years of Fermi/LAT data from NGC 1068 and NGC 4945, which count among the brightest Seyfert 2 galaxies. We search for potential variability of the high energy signal, and derive a spectrum of these sources. We also analyse public INTEGRAL IBIS/ISGRI data over the last seven years to derive their hard X-ray spectrum. We find an excess of high energy gamma-rays of 8.3 sigma and 9.2 sigma for 1FGL J0242.7+0007 and 1FGL J1305.4-4928, which are found to be consistent with the position of the Seyfert 2 galaxies NGC 1068 and NGC 4945, respectively. The energy spectrum of the sources can be described by a power law with a photon index of Gamma=2.31 \pm 0.13 for NGC 1068, while for NGC 4945, we obtain a photon index of Gamma=2.31 \pm 0.10. For both sources, we detect no significant variability nor any indication of a curvature of the spectrum. We discuss the origin of the high energy emission of these objects in the context of Seyfert or starburst activity. While the emission of NGC 4945 is consistent with starburst activity, that of NGC 1068 is an order of magnitude above expectations, suggesting dominant emission from the active nucleus. We, therefore, propose a leptonic scenario to interpret the multi-wavelength spectral energy distribution of NGC 1068.