Skymark is the only Japanese airline to have ordered the European superjumbo. It has said it will buy six A380s.
Finance Director Masakazu Arimori said the sizes of the interior fittings were slightly off and needed to be redone, meaning delivery for Airbus to fit them had been delayed.
Arimori blamed the cabin interior supplier, which Skymark declined to identify.
He estimated a delay of between 2.5 and six months to the delivery to Skymark of the first aircraft, which had been expected around the end of the year.
"We could squeeze the parts to fit, but it is a safety issue. We are in talks with Airbus about getting the work finished," he said.
A spokeswoman for Airbus declined to comment.
Airbus said in April the airline's first A380 had made its maiden test flight and would be delivered "later this year".
Word of the delay comes two weeks after Qatar Airways delayed taking delivery of its first A380 by "several weeks".
Qatar Chief Executive Akbar Al Baker told Reuters he had asked Airbus to address "issues with the interior of the cabin", after a pre-delivery customer inspection.
Skymark plans to use its A380s for discount business class flights overseas starting with New York.
Delays in airliner deliveries can cause disruption and extra cost for airlines as they reassign aircraft to fill gaps.
Airbus sales chief John Leahy said on Wednesday that Qatar would receive its first A380 "in the next couple of weeks".
Separately, Airbus said this week it had found signs of fatigue on fewer than 10 percent of the doors inspected on A380s after a number of reports of noise and that there was no immediate safety issue.