The human activities in the offshore oil and gas, renewable energy and construction industry require reliable data acquired by different types of hydrographic sensors: DGNSS (Differential Global Navigation Satellite System) positioning, attitude sensors, multibeam sonars, lidars or total stations installed on the offshore vessel, drones or platforms. Each component or sensor that produces information, unique to its position, will have a point that is considered as the reference point of that sensor. The accurate measurement of the offsets is vital to establish the mathematical relation between sensor and vessel common reference point in order to achieve sufficient accuracy of the survey data. If possible, the vessel will be put on a hard stand so that it can be very accurately measured using the standard land survey technique. However, due to the complex environment and sensors being mobilized when the vessel is in service, this may not be possible, and the offsets will have to be measured in sea dynamic conditions by means of a total station from a floating platform. This article presents the method of transformation by similarity with elements of affine transformation, called Q-ST (Quasi-Similarity Transformation). The Q-ST has been designed for measurements on such unstable substrates when it is not possible to level the total station (when the number of adjustment points is small (4–6 points)). Such situation occurs, among others, when measuring before the offshore duties or during the jack up or semi-submersible rig move. The presented calculation model is characterized by zero deviations at the adjustment points (at four common points). The transformation concerns the conversion of points between two orthogonal and inclined reference frames. The method enables the independent calculation of the scale factor, rotation matrix and system translation. Scaling is performed first in real space, and then both systems are shifted to the centroid, which is the center of gravity. The center of gravity is determined for the fit points that meet the criterion of stability of the orthogonal transformation. Then, the rotation matrix is computed, and a translation is performed from the computational (centroid) to real space. In the applied approach, the transformation parameters, scaling, rotation and translation, are determined independently, and the least squares method is applied independently at each stage of the calculations. The method has been verified in laboratory conditions as well as in real conditions. The results were compared to other known methods of coordinate transformation. The proposed approach is a development of the idea of transformation by similarity based on centroids.