ANA Group, Japan's largest airline, reported an 8.4 billion yen ($108 million) quarterly loss as travel declined after the earthquake in northeastern Japan.
All Nippon Airways said Friday that rising crude oil prices, which push up jet fuel costs, are also a challenge.
Consumer sentiment remains weak in Japan after the March 11 earthquake and tsunami devastated the country's northeast, dampening demand for travel.
ANA reported a loss of 5.2 billion yen in the April-June quarter of the previous year.
The number of passengers on ANA's Japan routes plunged 14.7 percent to 8.2 million during the quarter, offsetting the better results for passengers for its international flights, which rose 4 percent on year.
Quarterly sales dipped 1.7 percent to 305 billion yen ($3.9 billion).
ANA said fragile consumer confidence after the March disaster discouraged travel, but business travel began to recover after bottoming out in April.
International cargo grew because of the increase in transportation of emergency supplies such as medicine and water in response to the disaster, offsetting the cargo volume drop caused by auto and electronics parts suppliers getting damaged in northeastern Japan.
To deal with the fall, ANA reduced regular services and used smaller aircraft on many routes, it said. It also flew relief flights to the disaster-struck areas.