Context. The nearly edge-on galaxy NGC 4945 is one of the closest galaxies where an AGN and starburst coexist, and is one of the brightest sources at 100 keV. Near and mid-infrared spectroscopy have shown very strong obscuration of its central region, rivaled only in strength by some of the most deeply obscured ULIRGs. In addition, we mapped the S(1), S(2), and S(3) pure rotational lines of H 2 , which trace the distribution of warm molecular hydrogen. Finally, we obtained an extinction map (A V ) based on the apparent strength of the 9.7 μm silicate absorption feature. Results. At a spatial resolution of ∼5 , our extinction map traces the contours of the starburst ring. The highest extinction is, however, found at the nucleus, where we measure A V (9.85 μm) ≈ 60. Within the uncertainty of the astrometry, all emission lines are found to peak on the nucleus, except for the warm molecular hydrogen emission, which shows a maximum 60−100 pc NW of the nucleus. We favor a scenario in which the emission of the lower H 2 0−0 S(1) and S(2) rotational lines originate mainly in an unobscured extranuclear component associated with the super-wind cone observed in the HST NICMOS map of the H 2 1−0 S (1)