The Technical University of Crete comprises five Engineering Departments of innovative specialties as well as a Sciences Department. All the Departments run organized postgraduate study programmes (apart from the Architectural Engineering Department) and are as follows by year of establishment:

The mission of the Sciences Department is to provide scientific training to the students of the University in core subjects such as mathematics, mechanics, physics, chemistry and social sciences.

The Department of Production Engineering and Management, the first one to be established in Greece on this specialty, aims to educate engineers into scientists specialized in the design and the operational management of modern technological and administrative systems.

The Department of Mineral Resources Engineering focuses on educating engineers who are capable of covering a broad range of scientific and technical activities for the search, exploitation, enhancement and processing of mineral resources as well as environmental geotechnology.

Studies at the Electronic and Computer Engineering Department emphasize on the top technical training of its students in modern technology topics such as electronics, systems, information technology and telecommunications.

The Environmental Engineering Department aims to educate engineers who are experts in the management and protection of the environment.

The Architectural Engineering Department emphasizes on the cultivation and promotion through teaching and research of the scientific areas of architecture, urban planning and land use planning, architectural technology, protection and restoration of monuments and complexes as well as the environmental and ecological dimension of the architectural design.