Provided are an imaging device, an imaging method and an imaging control program which make it possible to shorten an imaging time, and to capture an image of each observation region at an appropriate focusing position regardless of the state of installation of a culture vessel on a stage. In a case where an observation target is imaged multiple times, a focusing position of an observation region within a culture vessel is detected by auto-focus control during first imaging, and the first imaging of each observation region is performed using the focusing position. Next, the focusing position of a reference position is detected by auto-focus control during second imaging subsequent to the first imaging, and the focusing position of each observation region detected in the first imaging is corrected on the basis of the detected focusing position and the focusing position of the reference position in the first imaging.