A transport status estimation system includes a storage unit configured to store container information in which a container ID and loaded cargo information, an input unit configured to receive input of tracking information, a specifying unit configured to specify which cargo in the loaded cargo information corresponds to the tracking target cargo according to a degree of coincidence between the loading time and the loading location of each cargo included in the loaded cargo information and the loading time and the loading location of the tracking target cargo included in the tracking information, and specify the container ID of the container in which a specified cargo is accommodated based on the container information, and an estimating unit configured to estimate a transport status of the tracking target cargo based on the container ID.