By Megumi Fujikawa 

TOKYO-- Skymark Airlines Inc. became one of the biggest victims of the yen's recent weakness, saying its plan to buy superjumbo jets when the currency was much stronger led to its bankruptcy protection filing.

The country's third largest carrier filed for court protection late Wednesday, six months after it was hit with a $700 million cancellation fee by Airbus when its order for six A380 planes was scrapped.

"When we made the contract with Airbus, the yen was around Yen80 (against the dollar)," the company's new chairman Takashi Ide said Thursday at a news conference. "Then the yen weakened rapidly to Yen120, inflating the cost (of the A380 deal)."

While Skymark intends to keep flying during an attempted rehabilitation, helped by a cash supply from Tokyo equity firm Integral Corp., its collapse into bankruptcy protection highlights one of the downsides of Prime Minister Shinzo Abe's economic policies.

Mr. Abe's drive to reflate Japan's economy has sharply weakened the yen, providing a tailwind for the nation's biggest exporters to hit record profits, such as Toyota Motor Co. For other companies the effect has been the opposite. Sharp Corp. recently said it would fall short of its Yen30 billion net profit forecast for the current business year ending March 31 due to the inflated prices of items it imports.

Now Skymark has become the poster child for smaller firms and import-reliant companies that are feeling the pain of the softer yen.

The budget airline, founded in 1996, said the weaker currency put pressure on its bottom line through the dollar-denominated costs of leasing aircraft and purchasing jet fuel from abroad. But it was Skymark's bold decision to buy the Airbus planes when the yen was at a peak in 2011 that exposed the airline to a currency risk that proved too large.

Mr. Ide said a request to postpone delivery of the planes, sparked Airbus's decision to scrap the order in July and charge a cancellation fee. The European plane maker initially asked for $700 million, but the two companies are still negotiating a final figure, he said.

"We are aware that Skymark Airlines has filed for bankruptcy protection. This is now a matter for the courts," Airbus said in a statement Thursday.

Skymark's lawyer said the firm's debts of Yen71 billion ($604 million) don't include the cancellation fee.

Hoping to emulate Japan Airlines' resurgence after seeking bankruptcy protection in 2010, Skymark will continue to operate flights, withdrawing from unprofitable routes to save about Yen50 million a month.

Masakazu Arimori, who took over as Skymark's president on Wednesday, said the airline would also like to continue with a three-party code-sharing deal with All Nippon Airways and JAL, adding that the company doesn't plan on any staff cuts for the time being.

"Currently, there are only three independent airlines that can base themselves at Haneda airport," Mr. Ide said, referring to ANA, JAL and Skymark operations at the Tokyo airport. "Unless we maintain our 36 (daily) slots at Haneda, those slots will be distributed to ANA and JAL, leading to higher airfares."

Shawn Schroter contributed to this article.

Write to Megumi Fujikawa at megumi.fujikawa@wsj.com

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