The first parts of the S-400 air defense system were flown to the Murted military air base northwest of Ankara on Friday, sealing Turkey's deal with Russia, which Washington had struggled for months to prevent.
"The U.S. and other F-35 partners are aligned in this decision to suspend Turkey from the program and initiate the process to formally remove Turkey from the program," said Ellen Lord, the under secretary of defense for acquisition and sustainment.
"The United States is spending between $500 and $600 million in non-recurring engineering in order to shift the supply chain," she said.
Used by NATO and other U.S. allies, the F-35 stealth fighter jet is the world's most advanced jet fighter. Washington is concerned that deploying the S-400 with the F-35 would allow Russia to gain too much inside information of the stealth system.
"The F-35 cannot coexist with a Russian intelligence collection platform that will be used to learn about its advanced capabilities," the White House said in a statement earlier on Wednesday.
Washington has long said the acquisition may lead to Turkey's expulsion from the F-35 program.
The Pentagon had already laid out a plan to remove Turkey from the program, including halting any new training for Turkish pilots on the advanced aircraft.
"The situation with Turkey is a government-to-government matter and we'll comply with any guidance issued by the United States Government," said a spokesperson for Lockheed Martin Corp , the prime contractor on the jet. Anna Ahronheim contributed to this story.