We present the analysis of ISO-Long Wavelength Spectrometer ( LWS ) observations of the two nearby late-type galaxies NGC1313 and NGC6946 . Both galaxies have been fully mapped in the [ CII ] Far-Infrared ( FIR ) fine structure line at 158 \mu m and some regions have been observed also in the [ OI ] ( 63 \mu m ) and [ NII ] ( 122 \mu m ) lines . We use these observations to derive the physical properties of the atomic interstellar medium , to establish how they relate with other interstellar medium components ( gas and dust ) , and how they vary with different galaxy components like nucleus , spiral arms and disk . The [ CII ] line is the main cooling line of the atomic medium . In NGC6946 and NGC1313 , its emission represents 0.8 \% of the infrared emission . Moreover , the [ CII ] emission can be spatially associated with three components : the nucleus , the star forming regions in spiral arms and the diffuse galaxy disk . This last component contributes \lesssim 40 \% in NGC6946 and \sim 30 \% in NGC1313 to the total emission . We apply the PDR model by Kaufman et al . ( ( 1999 ) ) to derive PDR physical parameters responsible for the neutral atomic gas emission ( G _ { 0 } , n and T _ { s } ) . The results do not significantly differ from what Malhotra et al . ( ( 2001 ) ) found by modelling the integrated emission of a sample of 60 normal galaxies . This suggests that the emission in each region under the LWS beam in NGC6946 and NGC1313 ( corresponding to a linear size of \sim 1.5 kpc ) is likely to arise from a mixture of components similar to the mixture producing the integrated emission of normal galaxies . However , some regions in NGC6946 have a G _ { 0 } / n ratio \sim 2–3 times smaller than the mean value found for the normal galaxy sample ( 1.3 ) , suggesting that the beam averaged contribution of a less active component in these regions is higher than its contribution in the integrated emission of normal galaxies or , conversely , that the bulk of the integrated emission of the normal galaxies is dominated by a few active regions probably located in their nuclei . CO ( 1–0 ) and [ CII ] in NGC6946 are well correlated and the mean [ CII ] /CO ratio agrees with the mean integrated ratios of the normal galaxies sample . This value ( \sim 500 ) is a factor \sim 2 less than the mean ratio found for a sample of normal galaxies observed with KAO by Stacey et al . ( ( 1991 ) ) . This difference is probably due to the fact that the KAO beam ( 55 \arcsec ) is smaller than the LWS beam ( 75 \arcsec ) , such that the Stacey et al . ( ( 1991 ) ) KAO observations are likely to be more biased towards the nucleus of the galaxies and therefore towards more active regions . In NGC1313 only 4 LWS regions have been observed in CO ( 1–0 ) , and three of them detected . The [ CII ] /CO ( 1–0 ) seems to systematically increase from the north-east to the south , along the S-shaped spiral arm , indicating that the interstellar medium conditions in NGC1313 are much more inhomogeneous than the conditions in NGC6946 . HI and [ CII ] in NGC6946 are completely de-correlated , probably because they arise from different gas components : [ CII ] arises principally in dense and warm PDR and HI from diffuse ( n \lesssim 3 \times 10 ^ { 3 } cm ^ { -3 } ) gas . On the other hand , in NGC1313 we successfully detect two distinct gas components : a cirrus-like component where HI and [ CII ] are weakly correlated as observed in our Galaxy , and a component associated with dense PDRs completely de-correlated form HI as observed in NGC6946 . Finally , we find that the HI residing in dense gas surrounding the star forming regions and presumably recently photo-dissociated , constitutes a few percent of the total HI . In turn , this dense gas component produces most of the [ CII ] emission emitted by the atomic neutral medium , even if its contribution is lower in NGC1313 than in NGC6946 . On the other hand , the [ CII ] emission arising from ionized gas is higher in NGC1313 than in NGC6946 .