ATS(Automatic Train Stop) system makes train stop when it runs over the speed limit and ensure the safe operation of train. Seoul Metro line 2 in Korea, which started its passenger service in 1982, has adopted ATS system for its signaling system. The ATS system has only a train stop function at the time of emergency, and Seoul Metro is planning to replaced them with ATC(Automatic Train Control)/ATO(Automatic Train Operation) system which can provide the dedicated speed control for headway reduction and automatic operation of train. Until all the ATS system is replaced with the new ATC system, both systems are to operate simultaneously at the same metro line. In this situation, ATS system sometimes reveals improper operation: train stops suddenly without any obstacles in front of it. These emergency stops cause interruption of passenger service, and abnormal abrasion of wheels and rail. This paper makes it clear that these interruptions are caused by EMI phenomena between ATS on-board device and ATC wayside device : Signal current flowing in AF track circuit of ATC is turn out to be a EMI source that prevent normal operation of the ATS on-board device. Although the two systems have different frequency-ranges (ATS system has frequency range between $78{sim}130$[kHz] and ATC system has frequency range between $9.5{sim}16.5$[kHz]), it turned out that EMI phenomena appears between the both systems. This is investigated by measuring the output signal from ATS on-board device passing over ATC wayside device. The FFT(Fast Fourier Transform) analysis of the signal reveals that AF track circuit signal is transmitted to the ATS on-board device and induce noise causing improper operation. The countermeasures to the EMI phenomena are examined in three ways; blocking EMI transmission, enforcement of EMS (Electromagnetic Susceptibility) of ATS on-board device, and blocking the EMI source. It is suggested that the practical solution be blocking EMI source temporarily, that is breaking AF track circuit signal when the trains with ATS on-board device pass over it. To this purpose, TODS(Train Occupation Detection System) is developed, and has made a success in preventing the EMI problem of Seoul Metro line 2.