The technical issues began around 6 a.m. local time, affecting automated check-in machines used for international departures, Kyodo News Agency reported.
The problem was resolved by approximately 11 a.m., Japan News reported.
The incident came after widespread delays and cancellations on April 21, when flights at Haneda were disrupted by a glitch in the air traffic control system.
The back-to-back disruptions raised concerns over system reliability at one of Asia’s busiest aviation hubs, although normal operations have since resumed.
Haneda Airport, officially Tokyo International Airport, was named the world’s third best airport after Singapore Changi and South Korea’s Incheon Airport in the 2026 ranking by London-based aviation organization Skytrax.