This paper presents a Fault Tolerant-Model Predictive Control (FT-MPC) for a vessel featured by the presence of a greater number of actuators with respect to the number of controlled outputs, classified in the category of over-actuated systems. Over-actuated plants are usually controlled by a main controller in conjunction with a Thrust Allocation (TA) algorithm in order to guarantee the required control performances. In this work an unconstrained Quadratic Programming (QP) TA policy is considered in conjunction with a MPC to drive the vessel. The proposed solution has been tested on an over-actuated vessel called Cybership II. The main contribution of this paper is the introduction in the MPC of a fault tolerant action, in order to improve control performance in actuators' fault scenarios. A Linear Parameter-Varying (LPV) model has been used to described the Cybership II dynamics and to develop the proposed controller. Considering this model, a MPC has been developed to drive the vessel, verifying controller performance in standard control scenarios. The proposed FT-MPC has been compared with respect to a standard MPC in actuators' fault scenarios, considering several wave noise disturbances. Reported simulation results show the effectiveness of the proposed approach.