A failure of All Nippon Airways' check-in systems at 50 airports across the nation led to the cancellation of dozens of domestic flights Tuesday affecting over 10,000 passengers.

The major carrier said the glitch hit at around 8:20 a.m. at all airports where it has services, bringing online check-ins and passenger confirmations at boarding gates to a standstill. The problem was resolved about three hours later.

ANA also suffered a problem with its check-in system at 48 domestic airports in February that caused delays of up to 40 minutes in the departure of some flights. The system was restored in 26 minutes but the cause remains unclear.

ANA is checking whether the latest incident is related in some way to the previous trouble.

Four other domestic airlines that share the same check-in system — Starflyer, Airdo, Solaseed Air and Ibex Airlines — also experienced the same trouble.

ANA had cancelled 87 domestic flights as of 12:30 p.m., including those that were scheduled to leave Sapporo, Haneda in Tokyo and Itami in Osaka Prefecture.

The departure of many other flights was delayed, affecting about 10,300 travelers.

Customers have also been unable to make reservations or check for vacancy via the Internet.

In a statement on its website the company said it "deeply apologizes" for the trouble as travelers were forced to waste time in long queues at the check-in counters of airports nationwide.

Hirotaka Kawata, who was trying to return to Kagoshima Prefecture from Haneda airport, was disappointed as he had already delayed his return by one day because a small plane's front landing gear failed, leaving it stranded on Kagoshima airport's runway, causing flight cancellations Monday.

"I changed my flight to this morning because of the runway closure at Kagoshima airport and now I'm going through more trouble," the 42-year-old said.