Air transport security deals with measures to protect against criminal and terrorist threats against civil aviation. After the events of 11 September 2001, NLR-ATSI has implemented a security research program that aims to reduce the threats related to:
- Airspace Security (protection of airspace / restricted zones);
- On-board Security (flight security procedures and aircraft security);
- Security on the Ground (ATM infrastructures and airports);
- Information and Communication Security (ATM systems and Airport IT systems).

The NLR-ATSI Security Strategy presents In-flight Security as key area in support of the Dutch government and the Air Transport Sector. Here, the focus of the Safety Institute is to develop security cases (including threat assessment and incident/accident analysis), new training concepts, and certification requirements. NLR-ATSI is well aware of the security regulations provided by international organisations like ICAO, EU, and ECAC.

NLR-ATSI and NLR knowledge and technologies in the fields of Military Aviation and Space can be used for e.g. border control, protection of infrastructures, and people (i.e. defence against terrorism). In this context, ongoing security related activities at NLR include research on Unmanned Aerial Vehicles in civil airspace, Self Protection, Ground stations and remote sensing, Earth observation, Electromagnetic Interference, and data protection.

Key NLR-facilities such as NARSIM, GRACE/G-FORCE, and TRADEF are used for simulation, validation, and training of security concepts and systems for protecting the whole chain of air transport: ATC, airports, and flight operations. The NLR research aircraft are available to perform trials of secure avionics systems, data links, Electronic Flight Bags. NLR-ATSI also maintains an Aviation Security Database and a Threat Assessment Methodology.

More details and examples on this topic can be found in the Example studies section.