A sample processing apparatus for performing a process including a plurality of steps on a sample, the sample processing apparatus sequentially processing a plurality of samples, is disclosed. The apparatus comprises a plurality of units corresponding to the respective steps in the process; a transfer section which transfers a sample to the units according to a flow of the steps; and a controller. Specifically, when an operation was not performed successfully, the controller interrupts the process for a sample that had not reached the location where the unsuccessful operation was performed while continuing the process for a sample that had already passed the location, retries the operation that was not performed successfully, and resumes the interrupted process when the retried operation has been performed successfully.