WASHINGTON (Reuters) -The U.S. Transportation Department said on Thursday it fined Emirates $1.5 million for operating flights carrying JetBlue Airways' designator code in prohibited airspace.

The department said that between December 2021 and August 2022, Emirates operated a significant number of flights carrying the JetBlue Airways code between the United Arab Emirates and the United States in airspace prohibited by the Federal Aviation Administration to U.S. operators. This conduct also violated a consent order issued in October 2020 fining Emirates for operating other flights in airspace under an FAA prohibition.

Emirates was ordered to pay $200,000 under the 2020 order and another $200,000 if it violated the order within a year.

An Emirates spokesperson said in a statement the airline had intended to operate the flights at or above the restricted level but that in flight, air traffic control did not give clearance to ascend or had instructed flights to operate below the level.

"Our pilots duly followed ATC (air traffic control) instructions, a decision which is fully aligned with international aviation regulations for safety reasons," it said.

JetBlue, whose code share with Emirates ended in 2022, declined to comment.

The department said flights at issue had traversed the Baghdad Flight Information Region below certain altitudes, which the Federal Aviation Administration has prohibited all U.S. air carriers, all U.S. commercial operators and code shares from operating without special permission. Emirates could face another $300,000 fine if it violates the rules again within a year.

The Emirates spokesperson said in the statement that the airline no longer operated flights with U.S. carrier codes over Iraqi airspace.

Emirates told USDOT it prioritizes the safety of passengers, employees, and other airspace users, adding the flights in question only operated below the allowed level "as a result of direct instructions from the relevant air traffic controllers" and in some cases to avoid a collision.

Emirates argued the pilots "were legally obliged to follow the instructions of the relevant air traffic controllers and any failure to comply with such instructions would have had significant safety implications," the department said.