The first batch of a Russian S-400 missile defence system has arrived in Turkey, a development likely to anger the US and put the struggling Turkish economy at risk of new sanctions.

Three planes carrying equipment for the reported £1.6bn system arrived in Ankara from Russia on Friday, the Turkish defence ministry said.

The delivery of parts will continue for several days at the Mürted Air Base and authorities will decide “how it will be used” once the system is made operational, Turkey’s defence industry authority said in a statement. It is not yet known where the S-400 will be deployed.

Turkey, a member of Nato, says it was forced to take the unprecedented step of buying the sophisticated Russian equipment in 2017 after the US refused to supply the alternative Patriot missile defence system.

The US has since warned that Ankara cannot have both the S-400 and US F-35 fighter jets, alternatively offering the Patriot system after all and threatening that the S-400 purchase will trigger US economic sanctions.

But Turkey, which is establishing closer ties with Russia, has refused to bow to pressure from Washington, calling it a matter of national sovereignty.

“We’ve always said regarding the S400s that it’s an agreement that has been finalised and the process continues to progress,” the Turkish foreign minister, Mevlüt Çavusoğlu, told reporters. “There’s no problem and the process will continue in a healthy way going forward.”

Although the US president, Donald Trump, expressed sympathy for the Turkish decision during a meeting with his Turkish counterpart Recep Tayyip Erdoğan on the sidelines of a G20 meeting in Japan last month, Washington has repeatedly said the S-400 purchase is incompatible with Nato systems.

Nato said on Friday it was “concerned” by Turkey’s acquisition of the S-400 missile defence system.

“Interoperability of our armed forces is fundamental to Nato for the conduct of our operations and missions,” an official in Brussels told AFP.

The US fears that if Turkey integrates the S-400 into its defences, sensitive data about the F-35, a new generation multi-role stealth fighter, could be accessed by Moscow.

Ankara has purchased 100 F-35s, but Washington has already stopped training Turkish pilots and given Turkey until the end of July to get its personnel out of the US.

Despite the stalled F-35 programme and the memory of last year’s US sanctions over the detention of an American pastor that sent the Turkish lira tumbling, Erdoğan has remained confident that Turkey will avoid US sanctions.