The existing intentional electromagnetic interference (IEMI) fault injection method based on continuous sinusoidal wave has a difficulty in injecting faults at a specific operation or time. This means that the obtained faulty outputs do not always satisfy a specific condition (e.g., time or number of error bytes) for performing fault analysis such as differential fault analysis (DFA). This paper presents a method for estimating the timing of fault occurrences caused by the above IEMI-based method, which make it possible to examine if an obtained faulty output is available for fault analysis. The idea of this method is to observe side-channel information such as EM leakage and estimate fault injection time from the detection of a characteristic change in the obtained waveform. To validate this method, we performed an IEMI fault injection experiment on actual cryptographic hardware (a side-channel attack standard evaluation board). From the obtained faulty encryption outputs and waveforms, we confirm that the fault injection time estimated by back-calculation of faulty outputs corresponded to that obtained by waveform analysis. We also demonstrate the validity of several non-invasive observation techniques for obtaining waveforms.