In previous studies, the authors performed the magnetic signature reconstruction of the marine ship Zodiak as part of the measurement campaign focused on recording magnetic data and the relative position of a ship during its passage over a magnetometer immersed on the testing ground. A high degree of representation of the magnetic signature was obtained. However, the recorded measurement data revealed new patterns of the multi-dipole model behavior that were not observed in the synthetic data based analyzes. It was assumed that the main factor influencing the abovementioned behavior of the model is the error in determining the geographical position of the ship in relation to the magnetometer. Therefore, another research was carried out to determine the relative position of the ship and the measurement device in sea conditions, in the area of the test site used in the previous study. For this purpose, two different classes of GPS receivers were used. The first receiver was the same as that used to determine the position of Zodiak in the previous measurement campaign, while the second receiver, treated as a reference, was a top-class geodetic receiver. The difference in indications between these two receivers gave a picture of the scale of errors in the data recorded during the previous measurement campaign. These errors are used in the article to analyze the effect of inaccuracies in determining the ship position on the quality of magnetic signature reproduction. Two types of signature reproduction error were introduced – the error based only on the data collected from the ship’s paths, and the error in the entire area of magnetic anomaly. The model of Zodiak was used to determine the value of the magnetic flux outside the paths. Profiles of differences in indications of GPS receivers at sea which were obtained from actual measurements were used to analyze the errors in determining the ship position. A measurable result of the work reported in the article is the map of the loss of quality of magnetic signature reproduction as a function of the ship position determination error, which can indicate the range of applicability of the model and the described method.