The far-infrared spectra (45-197 μm) of 28 low-luminosity young embedded objects have been studied in order to search for possible evolutive trends in the observed spectral features. The low-resolution spectra from 45 to 197 μm of 17 Class 0 and 11 Class I sources taken with the Long Wavelength Spectrometer (LWS) on board the Infrared Space Observatory have been used for this analysis. The most prominent features presented by these spectra are the [O I] 63 and 145 μm fine-structure lines and pure rotational lines from the abundant molecules CO, H2O, and OH. Clear differences are found, however, between the spectra of the two classes of objects. Water lines, which are prominent in the spectra of Class 0 sources, are not observed in Class I objects, with an upper limit 10-5 on the H2O abundance. Furthermore, the total cooling due to molecular emission in Class 0 sources is on average significantly larger than in Class I sources, while the cooling due to atomic oxygen is fairly constant among the two classes of objects. Finally, the total gas cooling as traced by the far-infrared lines (LFIR) is correlated with the bolometric luminosity for the Class 0 sample of sources, with an LFIR/Lbol ratio (~10-2) of about an order of magnitude larger than in Class I sources. We suggest that most of the observed emission lines originate from shocks at the base and along the source outflows. In such a case these results can be interpreted in terms of a change in the modality of the interaction between the protostellar jet and the circumstellar environment. During the Class 0 phase the impact of energetic flows with the dense ambient medium gives rise to a strong component of nondissociative C-type shock, while during the Class I phase such impact produces less energetic shocks with an enhanced dissociative J-type component. Finally, the low H2O abundance found in Class I sources can be explained by the action of the progressively less shielded interstellar UV field.