This letter considers the physical layer security of a pilot-based massive multiple-input multiple-output (MaMIMO) system in presence of a multi-antenna jammer. We propose a new jamming detection method that makes use of a generalized likelihood ratio test over some coherence blocks. Our proposed method utilizes intentionally unused pilots in the network. The performance of the proposed detector improves by increasing the number of antennas at the base station, the number of unused pilots and also by the number of the coherence blocks that are utilized. Simulation results show that in the MaMIMO regime, perfect detection is achievable even with a small number of unused pilots.