ABSTRACT We study the multiphase medium in the vicinity of the active galactic nucleus Centaurus A (Cen A). Combined high-resolution observations with the Atacama Large Millimeter/submillimeter Array (ALMA) and Chandra X-ray Observatory indicate that the hot X-ray emitting plasma coexists with the warm and cold media in Cen A. This complex environment is a source of CO lines with great impact for its diagnostics. We present the images from the two above-mentioned instruments covering the nuclear region (diameter of 10 arcsec, i.e. ∼180 pc), and we study the conditions for plasma thermal equilibrium and possible coexistence of cool clouds embedded within the hot X-ray emitting gas. Further, we demonstrate that the multiphase medium originates naturally by the thermal instability arising due to the interaction of the high-energy radiation field from the nucleus with the ambient gas and dust. We demonstrate that cold gas clouds can coexist in the mutual contact with hot plasma, but even colder dusty molecular clouds have to be distanced by several hundred pc from the hot region. Finally, we propose a 3D model of the appearance of the hot plasma and the CO line-emitting regions consistent with the Chandra image, and we derive the integrated emissivity in specific molecular lines observed by ALMA from this model. To reproduce the observed images and the CO line luminosity the dusty shell has to be ∼420 pc thick and located at ∼1000 pc from the centre.