In the specimen processing system in which each of a specimen input portion which inputs a specimen, a specimen processing portion which processes the specimen, a specimen recovery portion which recovers the processed specimen, and a specimen transporting line which transports the specimen between the specimen input portion, the specimen processing portion, and the specimen recovery portion, are connected to each other by a plurality of processing (analysis) units, the processing (analysis) unit is provided with a CPU that controls the operation, and provided with a mechanism control portion which receives an electric signal from the CPU and operates the mechanism parts in the processing unit, and the mechanism part control portion includes means which can supply and stop the power of one or more arbitrarily specified mechanism parts by the electric signal from the CPU.