Research and Development (R&D) organisation has different activity, employee’s characteristics, goals, and planning system from a non-R&D organisation. It requires Management Control Systems (MCS) that fit R&D activities. The study proposes four important core elements of MCS particularly for a R&D organisation: desired ends, actors, control implementation, and control tools. The study investigates the existence and the use of those core elements in R&D project from the Government units and the control systems implemented by three government units. The study finds the existence of desired ends to have qualitative characteristics and to use it to control the project direction and to limit the scientific boundary. The actor is found to be treated differently, and therefore the use of decision space to reduce domination of the actor over the controller is found to be implemented. The MCS is found to be implemented in three stages: Input, Process, and Output stage. All of the three government units use a formal control type with different control tools, control dimension, and value of representation.