In this paper we consider the multimode multiphoton Jaynes–Cummings model, which consists of a two-level atom, initially prepared in an excited atomic state, interacting with N modes of electromagnetic field prepared in general pure quantum states. For this system we show that under certain conditions the evolution of the Wigner function at the phase-space origin provides direct information on the corresponding atomic inversion. This relation is also valid even if the system includes Kerr-like nonlinearity, Stark shift effect, different types of initial atomic states as well as moving atoms. Furthermore, based on this fact we discuss for the single-mode case the possibility of detecting the atomic inversion by means of techniques similar to those used for the Wigner function.