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The leader of aerospace giant Boeing's defense division said Sunday that the company is still fighting through issues that have delayed the construction of two new Air Force One presidential aircraft.

Boeing received a $3.9 billion contract in 2018 to build two new 747-8 aircraft for use as Air Force One that would be delivered by December 2024, but the aircraft are delayed until at least 2027 and 2028.

Ted Colbert, head of Boeing Defense, Space & Security, said the company is dealing with supply chain, inflation, workforce and other challenges in building the airplanes, which are heavily modified versions of 747 airliners. Boeing has lost more than $2 billion on the program amid delays.

"Our team is fighting through a very, very challenging program – two very complex airplanes," Colbert said. "We've done a ton of investment in our workforce and training, efficiency, work on the factory floor."

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Boeing said the new Air Force One project has proven to be "very, very challenging" in several areas that have led to delays. (Max Mumby/Indigo / Getty Images)

The Boeing 747-8s that will eventually serve as Air Force One are designed to be an airborne White House that can fly in worst-case security scenarios, such as nuclear war, and are modified with military avionics, advanced communications and a self-defense system.

Last year, the Biden administration chose to modify, but continue with, an Air Force One paint scheme that resembles the current white with two shades of blue. The design dates back to the Kennedy administration and the Biden choice reverses a President Trump decision to switch to a red, white and blue scheme.

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Boeing has lost about $2 billion on the contract for two new Air Force One jets. (Paul Chinn/The San Francisco Chronicle via / Getty Images)

In December 2016, Trump extracted a promise from Boeing's CEO at the time, Dennis Muilenburg, that the cost of replacing Air Force One wouldn't be more than $4 billion. 

Current Boeing CEO Dave Calhoun later said that "critics were right" about saying the contract was priced too low.

The nonpartisan Government Accountability Office (GAO) said in 2022 that the Air Force One program risked further delay because of a tight labor market for mechanics, lower-than-expected security clearance rates and Boeing's need to switch to an alternative supplier for some interior work.

President Biden chose a design for the next Air Force One that will closely resemble the current one. (U.S. Air Force/Staff Sgt. Nicolas Erwin/DVIDS / Fox News)

Last year, Boeing and the Department of Defense investigated a security clearance lapse that resulted in hundreds of Boeing employees working on the secretive Air Force One planes with expired credentials for months or years before they were temporarily suspended from accessing those work areas after the documentation issue was discovered. 

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The lapsed "Yankee White" security clearances impacted about 250 employees. After the lapse was discovered, the Air Force and Boeing worked to reinstate those clearances, with nearly all regaining current, valid Top Secret clearances and no workers losing their clearances. Boeing said at the time the issue had no impact on the timeline for the new Air Force One jets.

Reuters contributed to this report.