The Transportation Ministry, Israel Airports Authority, and the IDF have completed the implementation of directives and coordination procedures for Ben-Gurion Airport operations under the threat of missiles and drones. An advanced command and control system has been implemented to allow Ben-Gurion Airport to continue operating during missile and drone threats.

The system synchronizes threat monitoring, air traffic management, and the operations of all air defense systems. It instructs pilots to remain on the ground or continue circling in the air based on the most recent security assessment. Military officials stated that Israel has developed an operational capability that enables precise windows for takeoffs and landings.

The system relies on the operational experience of pilots employed by Israeli civilian airlines, many of whom serve or have served as reserve pilots in the IDF. The decision to keep the airport open remains subject to ongoing assessments. These measures aim to maintain aviation functionality while addressing security risks associated with aerial threats.

In June 2025, Israeli airspace was closed for 14 days during the Iran campaign, stranding tens of thousands of Israelis abroad and exposing systemic unpreparedness for prolonged conflicts. This event directly prompted the development of the current airport coordination system. The Israel Airports Authority initiated the construction of the Main Control Unit at Ben-Gurion Airport in 2025 to centralize air traffic management and defense coordination.

Ben-Gurion Airport's passenger numbers dropped 44% from 24 million in 2024 to 13.9 million in 2025, with flights declining from 144,000 in 2023 to 102,000 in 2025, according to the 2025 state audit. The 2026 state audit report explicitly cited the lack of a long-term war scenario as a critical gap in the Transportation Ministry and Civil Aviation Authority's preparedness. The Transportation Ministry faced legal scrutiny in 2024 for failing to update emergency aviation plans after the October 7, 2023, Hamas attack.