The Trump administration has confirmed that NATO ally Turkey will be removed from the F-35 Joint Strike Fighter program after it began accepting deliveries of the Russian-made S-400 surface-to-air missile system, which Moscow calls the "F-35 killer."

While President Donald Trump called it "a very tough situation," he said sales of the stealth jet to Turkey would no longer be an option due to its pursuit of the S-400.

"We are now telling Turkey that because you have really been forced to buy another missile system, we're not going to sell you the F-35 fighter jets," he confirmed before a cabinet meeting at the White House.

"With all of that being said, we're working through it. We'll see what happens, but it's not really fair. They wanted to buy. I don't stick up for countries. I don't stick up for Turkey," Trump said, adding he still has a "good relationship" with Turkish President Recep Tayyip Erdogan.

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Speaking to lawmakers Tuesday, Army Secretary Mark Esper, Trump's nominee to become defense secretary, called Turkey's decision to purchase the S-400 the wrong choice.

"They have been a long-standing and very capable NATO ally, but their decision on the S-400 is the wrong one," he said during his confirmation hearing before the Senate Armed Services Committee. "It's disappointing."

Esper's response to lawmakers was the first public comment by a Pentagon official on the matter since Turkey and Russia announced the deliveries last week.

Retired Air Force Lt. Gen. Chris Bogdan, former program executive officer (PEO) for the F-35 program, agreed with the administration that Turkey needs to exit the program to protect the integrity and security of the F-35.

"The S-400 system and the F-35 are not compatible, and there's too much at stake with the F-35 for the U.S. government not to do something about it," he said during an interview with Military.com.

Bogdan, who was the JPO chief between 2012 and 2017, was replaced by Vice Adm. Mathias W. "Mat" Winter in the job. Winter retired last week.

"When I was the PEO, we saw this coming. And the previous administration had discussed it and, diplomatically and politically, they tried hard to avoid it," Bogdan said during a phone call Tuesday. "And I don't know about this administration and what it's done to try and avoid it. But now we're … faced with a very tough decision."

Trump has repeatedly blamed the Obama administration for the U.S. finding itself in this dilemma, saying it didn't supply Turkey with the Patriot missile system battery, made by Lockheed Martin Corp. and Raytheon Co. However, officials have touted the Patriot to Turkey for years.

Turkey expressed interest in the system at one point after the war in Syria began in 2012. However, Erdogan insisted on also getting a technology transfer so that Turkey could someday build its own SAM system, according to Bloomberg news. The Obama administration declined.

But these type of risks -- sometimes foreseen -- within a high-level program are not unique, Bogdan said.

"The dilemma of a partner leaving the program is not new to the F-35 [Joint Program Office]," he said, referencing troubles the U.S. has had getting Canada to commit to the program.

"I would suspect that the JPO, in concert with the other parts of the U.S. government, were not surprised by this necessarily and have a set of courses of actions that they're working through," he said about the Turkey fallout.

"What is different about this situation is that Turkey's already bought airplanes and committed to buying the airplanes, but now they've committed to buying a radar system that is totally incompatible with having both the F-35 and that radar system," he said.

Turkey's decision to buy the S-400 has been in the works for years. In 2017, it firmed up a verbal agreement with Russia to purchase the S-400, known as the "Triumf." It came after relations between Turkey and Russia had slowly begun to ease: Erdogan in 2016 formally apologized to Russian President Vladimir Putin for the shootdown of a Russian Sukhoi Su-24 bomber aircraft over Turkish airspace in 2015.

Since then, Pentagon leaders, lawmakers and State Department officials have raised concerns over the vulnerabilities posed should Turkey operate the F-35 and S-400 simultaneously.

Most notably, Under Secretary of Defense for Acquisition and Sustainment Ellen Lord during a June 7 briefing with reporters said that prolonged proximity between the F-35 and S-400 systems might allow the SAM to "understand the profile" of the jet.

Lawmakers in recent months have pointed out the national security threat this could pose to U.S.-made systems.

Officials from both the Pentagon and Lockheed Martin, the F-35's manufacturer, told Military.com in recent weeks that they are looking to mitigate or track any risks to the program that could arise.

Those risks could include costs, production facility setbacks or production mismanagement from a supplier.

Turkish industries produce 937 parts for the F-35, including items for the landing gear and fuselage.

There is a little bit of wiggle room. It takes three to four years to build an F-35, so there is time to play catch-up should an entire production line close down, a Defense Department official, speaking on background, said Friday.

The U.S. will look to American suppliers for the time being as Turkey slowly exits the program, the official said.

The plan is to cancel contracts with Turkey by early 2020, according to Lord.

-- Oriana Pawlyk can be reached at oriana.pawlyk@military.com. Follow her on Twitter at @Oriana0214.