Magnetic anomaly generated around a ship is mainly due to the permanent magnetization(PM) and induced magnetization (IM) remaining on the hull. It is very difficult to predict the direction and its magnitude of the permanent magnetization distributed over the hull, that is caused by mechanical or thermal stress. In this paper, an effective method is proposed to separate two components, the one produced by PM and the other by IM, from the underwater earth field signal distorted by the ferromagnetic material of the ship. The method can easily provide the two kinds of magnetic anomaly through exploiting experimental results and 3D electromagnetic field analyses even though the PM distribution on the hull is not known. To validate the proposed method, a model ship is manufactured and tested. The results would be of much help to basis research for securing safe navigation of a ship against dangerous factors in underwater.