Sea-keeping, maneuvering, and motion tests of surface vehicle/ship model need self-propelled scale model which can perform different maneuvers. The present work describes the design implementation and testing of embedded system of an autonomous system for unmanned surface vehicles (USVs)/ship model in the laboratory environment. This is a first-time national development test in the wave basin has demonstrated full-free running self-controlled model in a disturbance environment. The central unit of the system is an embedded controller, compact reconfigurable input–output (cRIO) which features a field-programmable gate array (FPGA) and a processor running Linux-based real-time operating system. It performs the main propulsion control, rudder control data logging and telemetry. The peripherals are interfaced with main controller through multifunction input–output module. The RS-232 communication is used to interface the MRU sensor with main controller. LabVIEW is used as programming tool to develop a program to control the peripherals connected to the main controller and data acquisition over a wireless link using Wi-Fi. A graphical user interface is developed to send control commands and visualize the 4-degree of motion at base station in real time. © Springer Nature Singapore Pte Ltd. 2019.