The organisation chart of the laboratory involves 3 well-defined responsibility levels. Firstly, the laboratory relies on the direction of the Director General (D-G). The Director-General is the chief executive officer of INL as well as its legal representative. He or she reports to the Council and directs the laboratory acting under the auspices of the INL Staff Rules & Regulations, INL financial administration rules and INL statutes. The D-G counts on the support of the Deputy Director General (DD-G), who is also designated by the Council. Initially, the DD-G's specific responsibilities include assisting the DG in the day-to-day work and in the scientific development of INL, working in strong cooperation with the Research and Infrastructure Directors and reporting to the INL D-G. The D-G will work closely with a group of experts in legal, financial, communication and scientific issues who will also be part of INL staff. Additionally, the D-G will work with two strategic organs (scientific and finance committees) depending on the needs of the laboratory. The entire structure of this first level of responsibility is related to the strategy, public image and general governability of the laboratory.

At a second level of responsibility, the organisation chart presents the INL Board of Directors (B-D). The INL has four directors: Administration, Industrial Liaison & Technology Transfer, Research and Scientific & General Infrastructure. Each of them will oversee the staff and departments under his or her responsibility. All directors from the B-D will report to the D-G, acting as a solid connection between the D-G and the daily operations and activities of the entire INL staff.

Finally, the INL organisation chart includes the INL departments. At this level of the organisation, Department Officers (D-O) will lead small administrative working teams. D-Os will be in charge of projects, reporting directly to their directors. Regarding the departments of the four strategic research areas of INL (nanomedicine, environmental control & food monitoring, nanoelectronics and nanomachines & nanomanipulation), each of them will have a Scientific Coordinator who will work closely with INL Principal Investigators. All together, they will foster the interdisciplinary work and the cooperation of all INL research groups.