A control system automates control of reefer container resources in a reefer container system including a remote server computer in communication with reefer containers. Each reefer container includes a refrigeration system to control a climate of an interior cargo compartment of the reefer container. The refrigeration system includes a refrigeration circuit, including a compressor, a cooling space, and sensors to measure or estimate refrigeration system readings. The refrigeration system transmits refrigeration system parameter data; the remote server computer obtains the parameter data acquired during operation of the refrigeration system from at least one reefer container, and estimates a condition of the refrigeration system, including determining whether an alarm has been issued, or whether the estimated reefer container condition indicates that the refrigeration system requires maintenance or testing. A reefer container resource control unit receives the reefer container condition to automatically allocate the reefer container based on the reefer container condition.