We observed the CO(3-2) emission of the emission-line regions HubbleI, HubbleV, HubbleX, Holmberg 18, and the stellar emission-line object S28 in NGC6822 with the ESO Atacama Pathfinder Experiment (APEX) 12m telescope as part of its science verification. The very low system temperature of 130-180K enabled us to achieve detections in 4 single pointings and in a high spatial resolution 70x70 map of HubbleV. We compare the spectra with HI observations, obtained with the Australia Telescope Compact Array, of the same regions. In combination with previous multi-line CO observations, we perform a preliminary investigation of the physical conditions in HubbleV using a simple LTE model. We estimate the mass of the HubbleV region and the H_2/I_CO(3-2) conversion factor. Also, we show that HubbleV is located very near the line-width versus size relation traced by the Milky Way and LMC molecular clouds.