This article describes the development of control system of robotic complex for constructions and buildings printing. Based on analysis of existing approaches authors propose the solution for control system development for 3D-printer with gantry-type construction, which can move on rails. Fully functional model of the control system was created by authors. It includes graph in the form of Petri net for research of system elements operation. This approach allows the control system to prevent the emergency situations in real-time when the failure or obstacles sensors are triggered. It also provides the desired positioning error within 10 mm and control of uniform printing using laser distance sensor mounted on the end effector. To test the efficiency of control algorithm of main movement module authors have developed simulation model of the control system using Matlab and studied reaction to safety sensor triggering and extruder positioning error. Model confirms the possibility of proposed algorithm usage in real device.