NATO said Friday it was "concerned" by Turkey's acquisition of Russia's S-400 missile defence system after Ankara took delivery of its first batch.

The alliance has repeatedly warned Turkey that the Russian system is incompatible with other NATO weapons systems, not least the F-35 fighter jet.

"We are concerned about the potential consequences of Turkey's decision to acquire the S-400 system," a NATO official told AFP.

"Interoperability of our armed forces is fundamental to NATO for the conduct of our operations and missions."

The US fears that if NATO member Turkey integrates the S-400 into its defences, there is a risk that sensitive data about the F-35, a new generation multi-role stealth fighter, could leak back to the Russians.

President Donald Trump's pick for Pentagon chief, Mark Esper, confronted the Turkish defence minister about the deal on the sidelines of a NATO meeting last month.

Washington has threatened to expel Turkey from its F-35 programme, giving Ankara until July 31 to cancel the S-400 purchase or have its pilots kicked off the training course and expelled from the US.

But Turkish President Recep Tayyip Erdogan has refused to back down and said he is confident Turkey will not face US sanctions.