Aims. We investigate the structure and shape of the photospheric and molecular layers of the atmospheres of four Mira variables. Methods. We obtained near-infrared K-band spectro-interferometric observations of the Mira variables R Cnc, X Hya, W Vel, and RW Vel with a spectral resolution of about 1500 using the AMBER instrument at the VLTI. We obtained concurrent JHKL photometry using the the Mk II instrument at the SAAO. Results. The Mira stars in our sample are found to have wavelength-dependent visibility values that are consistent with earlier low-resolution AMBER observations of S Ori and with the predictions of dynamic model atmosphere series based on self-excited pulsation models. The corresponding wavelength-dependent uniform disk (UD) diameters show a minimum near the near-continuum bandpass at 2.25â€‰ μm. They then increase by up to 30% toward the H2O band at 2.0â€‰ μm and by up to 70% at the CO bandheads between 2.29â€‰ μm and 2.48â€‰ μm. The dynamic model atmosphere series show a consistent wavelength-dependence, and their parameters such as the visual phase, effective temperature, and distances are consistent with independent estimates. The closure phases have significantly wavelength-dependent and non-zero values at all wavelengths indicating deviations from point symmetry. For example, the R Cnc closure phase is 110°â€‰ ± â€‰ 4° in the 2.0â€‰ μm H 2O band, corresponding for instance to an additional unresolved spot contributing 3% of the total flux at a separation of ~4â€‰ mas. Conclusions. Our observations are consistent with the predictions of the latest dynamic model atmosphere series based on self-excited pulsation models. The wavelength-dependent radius variations are interpreted as the effect of molecular layers lying above the photosphere. The wavelength-dependent closure phase values are indicative of deviations from point symmetry at all wavelengths, thus a complex non-spherical stratification of the extended atmosphere. In particular, the significant deviation from point symmetry in the H2O band is interpreted as a signature on large scales (there being a few across the stellar disk) of inhomogeneities or clumps in the water vapor layer. The observed inhomogeneities might possibly be caused by pulsation-and shock-induced chaotic motion in the extended atmosphere.