In order to reveal physical conditions of molecular gas in active galaxies (active galaxies mean both starbursts and AGNs in this paper), we carried out systematic observations (R = 19 ~ 120) of CO funda- mental band at 4.7 m in absorption with AKARI. We also made follow-up CO absorption observations at higher spectral resolution (R = 5000 ~ 1000) with Subaru. Recently, Herschel made extensive ob- servations of highly-excited CO lines in emission in the far-infrared. The two data sets (absorption and emission) sometimes provide us with apparently inconsistent results. One case is starburst galaxies: Sub- aru observations showed low temperature of molecular gas toward the starburst NGC 253, while Herschel detected highly excited CO lines in the starburst. This suggests that warm molecular clouds are more deeply embedded than newly formed star clusters. The other case is obscured AGNs; Herschel detected highly excited CO lines in emission in nearby AGNs, while AKARI and Subaru observations showed CO absorption only in some of the obscured AGNs. This could re ect the dierence of nature of molecular tori in these AGNs. We propose the combination of the absorption and emission observations as an eective tool to reveal geometry of warm molecular clouds in active galaxies.