The Department for Computing and Control Engineering is comprised of three sub-departments: The Sub-department for Automatic Control and Systems Engineering, The Sub-department for Applied Computer Science and Informatics and The Sub-department for Computer Engineering and Computer Communications. Within the Department there are 20 laboratories in total.

The Sub-department for Automatic Control and Systems Engineering is in its scientific research work focused on the field of automatic control and systems engineering, biomedical engineering and geo-information systems and technologies.
The Sub-department for Applied Computer Science and Informatics is in its scientific research work focused on the field of programming languages and translators, operative systems, web programming, software engineering, computer aided business, intelligent systems and soft computing.

The Sub-department for Computer Engineering and Computer Communications is in its scientific research work focused on the fields of computer architecture and computer networks,  real time programming, computer based systems, FPGA and DSP technologies, programme support in multimedia systems and cell phone industry and the programme support in audio and video signal processing.
Apart from the enlisted organizational units, the Department organizes the activities of the Geo-Information Technologies and Systems Center, whose activities, in the most general terms, include the management of spatial resources. The center has the following organizational-technological units: The Department for System Support, The Laboratory for the Acquisition, Processing and Presentation of Geo Spatial Data, The Laboratory for Sub Terrestrial Detection, The Laboratory for GIS and Software Development.