This paper presents an automatic, rigorous, and robust method to determine a Multi-Beam Echo Sounder (MBES) and Inertial Measurement Unit/Inertial Navigation System (IMU/INS) latency calibration. The latency may be due to the IMU/INS itself, but also to the time-tagging configuration, which is generally left to the survey systems user. One survey strip over a flat seafloor is the required configuration of line for using this approach, called Multibeam IMU/INS Latency Automatic Calibration (MILAC), standing for MBES to IMU/INS Latency Automatic Calibration. The algorithm considers only data with maximum latency effects and integrates an automatic data selection for this purpose. The latency estimation procedure is based on an iterative Least Square adjustment method followed by a statistical analysis. Our process can deal with beam acoustic refraction caused by the speed of sound in sea water. The accuracy of MILAC is about 2 ms (millisecond) and its average precision of 0.15 ms. MILAC is able to determine the latency with an average resolution of 5 ms. However, the morphology of the survey line is restricted to smooth and regular seafloor and the survey platform should have a relatively high attitude rate.