A semi-automatic mode according to which an operator makes a necessary confirmation when an image pickup condition for a micro image is set with reference to a macro image is provided in controlling the acquisition of the macro image, the setting of the image pickup condition, and the acquisition of the micro image with respect to each of a plurality of samples S stored in a sample storage unit 11, and in the semi-automatic mode, the sample S whose macro image has been acquired by a macro image acquiring unit 20 is placed at a standby position without being moved directly to an image acquiring position for a micro image acquiring unit 30. According to this structure, image acquisition with respect to each of the samples S can be efficiently performed, and an operational burden imposed on the operator is reduced. Accordingly, it becomes possible to realize an image acquiring apparatus, an image acquiring method, and an image acquiring program each of which is capable of performing image acquisition with respect to each of the samples with high efficiency.