Japan Airlines (JAL) officials said Wednesday they have overcome a glitch in their passenger check-in system for domestic flights, although 32 domestic flights were canceled and 2,500 passengers were adversely affected.

According to the airline, a system failure that began at around 6:50 am local time meant that throngs of passengers had to battle queues and try to check in manually at airports.

The furor among passengers was due to a glitch apparently knocking out airports' automated systems including the use of QR-codes to check in for reserved flights and automatic check-in machines at airports such as Haneda in Tokyo.

The system problem caused delays of up to two and a half hours for some domestic JAL flights and around 2,500 passengers were affected by the system error.

JAL officials said the problem was rectified by around 10:00 am local time and believed a network error was to blame, possibly stemming from one of two servers not operating properly.

The officials said that after ascertaining that one of its two servers related to automated check-ins had potentially malfunctioned, they disconnected the problematic server, which helped restore operations to normal.

The company is still looking into the cause of the glitch and the potentially faulty server and said that as a result of the system failure, 32 flights to and from Tokyo, Osaka, Fukuoka and Sendai have been canceled.

Local media quoted some irate passengers as saying that JAL failed to communicate with them effectively about the problem and relay information efficiently about the lengthy delays.

Others said they were completely left in the dark by JAL with no information provided at all as to the cause and length of the delays, as they were left queuing at oversubscribed counters to check in for flights that they later found had been canceled.