In this paper we consider 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 the initial atomic state as well as moving atom. 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 Wigner function.