Acting Pentagon chief Pat Shanahan has warned Turkey over plans to buy a Russian missile defense system, while a US senator has asked whether Ankara is seeking to leave NATO.

Turkey has rejected a US proposal to deliver one Patriot missile defense system by the end of 2019 provided that Ankara abandons a deal to buy the S-400 missile defense system from Russia.

Shanahan warned that the purchase would imperil prospects to sell the NATO ally the next-generation F-35 jet Turkey is helping to build.

"My position is that the S-400 and F-35 are incompatible – meaning that they don't go together," Bloomberg quoted him as saying in an interview in his Pentagon office.

Turkey signed a contract worth $2.5 billion in December 2017 for the purchase of the S-400 missile defense system, ignoring objections from its NATO allies.

Foreign Minister Mevlut Cavusoglu on Saturday said that Turkey bought the Russian-made system, as it could not buy a similar one from its Western allies.

The purchase reflects a broader political shift as President Recep Tayyip Erdogan finds himself increasingly at odds with the US.

President Donald Trump has raised tariffs on Turkey, declined to extradite a Turkish cleric whom Erdogan blames for a failed coup in 2016 and infuriated Ankara over US support for Kurdish militants in Syria.

Shanahan did not say what action the US would take if Turkey went ahead with the purchase of the sophisticated defense system.

"We'll cross that bridge when we get there, but we are talking about making sure they have" US-made Patriot air defenses, he said.

The Pentagon chief said he has spoken with his Turkish counterpart Hulusi Akar five times since becoming the acting defense secretary on January 1.

"They're a strategic partner and I think at the end of the day, they'll remain a strategic partner," Shanahan said.

Military aircraft are parked at Incirlik Air Base in Adana, Turkey, which the US uses as the main staging ground for airstrikes in the Middle East.

The F-35 is the US's costliest weapons system and Turkey is a crucial participant in the program.

Turkish companies are reportedly set to produce about $12 billion in parts for the fighter jet, including key components such as the center fuselage and some landing gear.

According to an unclassified summary of a Pentagon report sent to Congress in November, Turkey risks expulsion from the F-35 program if its government takes delivery of the Russian system.

On Saturday, a US Senator called on Trump to cancel the sale of F-35 fighter planes to Turkey if the latter retains the S-400 purchase deal with Russia.

Democratic Senator Chris Van Hollen said the US should not allow Turkey to jeopardize the safety of US pilots and the security of NATO by using F-35 jets and S-400 missile systems at the same time.

American officials are concerned that sensitive F-35 technology designed to evade such a system could be compromised and used to improve Russia's air defense system if Turkey ends up with both systems.

The senator also questioned Ankara’s commitment to NATO.

Trump needs to make it crystal clear: If Turkey purchases the Russian S-400 system from Putin, it will not receive the F-35. Period. Turkey must not be allowed to compromise the safety of our pilots and the security of NATO. Do they want to quit NATO? https://t.co/pp0DuSFTG8

— Chris Van Hollen (@ChrisVanHollen) March 2, 2019

Erdogan has already pointed out that despite membership in NATO, Turkey “has a right to use different air defense systems” and that the US and others have no right to criticize Ankara for its military purchases.