The technology of robotic spacecrafts has been identified as one of the most appealing solutions to the on-orbit construction of large space structures in future space missions. As a prerequisite of a successful on-orbit construction, it is needed to use small autonomous spacecrafts for the transportation of flexible elements. To this end, the paper presents an energy-based scheme to control a couple of robotic spacecrafts carrying a flexible slender structure to its desired position. The flexible structure is modelled as a long beam based on the formulation of absolute nodal coordinates to account for the geometrical nonlinearity due to large displacement. Meanwhile, the robotic spacecrafts are actuated on their rigid-body degrees of freedom and modelled as two rigid bodies attached to the flexible beam. The energy-based controller is designed using the technique of energy shaping and damping injection such that translational and rotational maneuvers can be achieved with the suppression of the flexible vibrations of the beam. Finally, numerical case studies are performed to demonstrate the proposed schemes.