During measurements, the crankshafts of marine engines are usually supported on a set of rigid prisms. Such prisms maintain a constant height position, cause different values of reaction forces and, consequently, may cause elastic deformations of the crankshafts. Thus, the measurements of the dimensions and geometry of the crankshaft may be distorted. This article proposes a measuring system developed to support the crankshaft with a set of flexible supports. These supports implemented the given reaction forces, which ensured the elimination of the crankshaft deformations, regardless of the possible deviations, i.e., in the coaxiality of the main crankshaft journals. The values of these forces were calculated using the finite element method (FEM). These calculations showed that in order to eliminate the crankshaft deformations, the values of the reaction forces must change not only on individual supports, but also with the change of the shaft rotation angle during the measurement. The numerical experiments showed that the application of flexible supports results in uniform contact reaction forces on adjacent main journal supports. This uniformity occurs regardless of the quality of the crankshaft geometry. Thus, the necessity to use a set of flexible supports for measuring marine engine crankshafts was confirmed. The research also showed that the values of the reaction forces ensuring the elimination of shaft deflections under the assumption of nodal support can be treated as corresponding to the resultant reaction forces realized by the prismatic heads.