The rail fastening system forms an integral part of rail tracks, as it maintains the rail in a fixed position, upholding the track stability and track gauge. Hence, it becomes necessary to monitor their conditions periodically to ensure safe and reliable operation of the railway. Inspection is normally carried out manually by trained operators or by employing 2-D visual inspection methods. However, these methods have drawbacks when visibility is minimal and are found to be expensive and time consuming. In the previous study, the authors proposed a train-based differential eddy current sensor system that uses the principle of electromagnetic induction for inspecting the railway fastening system that can overcome the above-mentioned challenges. The sensor system includes two individual differential eddy current sensors with a driving field frequency of 18 kHz and 27 kHz respectively. This study analyses the performance of a machine learning algorithm for detecting and analysing missing clamps within the fastening system, measured using a train-based differential eddy current sensor. The data required for the study was collected from field measurements carried out along a heavy haul railway line in the north of Sweden, using the train-based differential eddy current sensor system. Six classification algorithms are tested in this study and the best performing model achieved a precision and recall of 96.64% and 95.52% respectively. The results from the study shows that the performance of the machine learning algorithms improved when features from both the driving channels were used simultaneously to represent the fasteners. The best performing algorithm also maintained a good balance between the precision and recall scores during the test stage.