A sample processing apparatus, including: a sample processing unit for obtaining a sample from a sample container positioned at a sample obtaining position and performing a predetermined process of the sample; a transport unit for transporting a sample rack holding the sample container via the sample obtaining position; and a transport controller for performing a stop process to stop the transport operation of the sample rack by the transport unit when a transport suspension event has occurred during the transport operation of the sample rack, and for controlling the transport unit to restart the transport operation of the sample rack from a stop position at which the sample rack has been stopped by the stop process.