Security of certain locations is of utmost importance. The contemporary works cater to locate the perturbations for the land based installations using the fiber optic based sensors. Intrusion detection for underwater environment is quite critical because of the high false alarm rates. Phase-optical time domain reflectometer (Φ-OTDR) has recently become prominent as it supports distributed acoustic sensing (DAS) utilizing optical fiber as a sensor. The benefit of developing a numerical model of the actual sensing system is that it mimics the strain developed in the fiber due to external acoustic perturbation which in turn changes the characteristics of the Rayleigh backscattered wave. Hence, we propose a numerical model based on the coherent Φ-OTDR set-up for undersea perturbation detection and classification. An intruder model is developed that determines the received pressure level at the fiber (sea depth) by considering the total transmission loss due to the simultaneous ships sailing at a pre-established distance from one another. The efficacy of the numerical model of the Φ-OTDR system is determined by firstly matching it’s outcomes with the experimental results for multiple sinusoidal disturbances acting at different locations on the fiber. Further, the numerical model is used to detect different ship sounds in underwater environment using feature extraction and frequency–time–energy relation. In addition, a complete pipeline to classify type of intruders is stated in detail.