Aims. We study the physical properties and amount of molecular gas in the central regions of galaxies with active nuclei. Methods. Maps and measurements of the J = 1-0, J = 2-1, J = 3-2, J = 4-3 (CO)-C-12, the J = 1-0, J = 2-1, and J = 3-2 (CO)-C-13 lines in the central arcminute squared of NGC 1068, NGC 2146, NGC 3079, NGC 4826, and NGC 7469, as well as 492 GHz CI maps in three of these are used to model the molecular gas clouds in these galaxies. Results. Bright CO concentrations were detected and mapped in all five objects. In all cases, the observed lines could be fitted with two distinct gas components. The physical condition of the molecular gas is found to differ from galaxy to galaxy. Rather high kinetic temperatures of 125-150 K occur in NGC 2146 and NGC 3079. Very high densities of 0.3-1.0 x 10(5) cm(-3) occur in NGC 2146, NGC 3079, and NGC 7469. The CO to H-2 conversion factor X is typically an order of magnitude less than the "standard" value in the solar neighborhood. The molecular gas is constrained within radii between 0.9 and 1.5 kpc from the nuclei. Within these radii, H-2 masses are typically 1.2-2.5 x 10(8) M-circle dot. The exception is the (relatively nearby) merger NGC 4826 with R = 0.3 kpc, and M = 3 x 10(7) M-circle dot. The H-2 mass is typically about one per cent of the dynamical mass in the same region.