General Petr Pavel, chairman of NATO’s Military Committee, sent a threat to Ankara saying the move to buy the S-400 system, would see the nation blocked from being part of any integrated air-defence system with NATO allies.
He said: “The principal of sovereignty obviously exists in acquisition of defence equipment, but the same way that nations are sovereign in making their decision, they are also sovereign in facing the consequences of that decision.”
Turkey is yet to sign on the dotted line over the deal, but Mr Pavel said it is “fair among allies to have that discussion, to raise all concerns and potential difficulties”.
The UK and US have raised concerns over the deal, which could see the S-400 system gain information about the F-35 Joint Strike Fighter programme, which is central to the future air power of several NATO nations.
At the time of announcing the deal, President Recep Tayyip Erdogan remained defiant.
He said: “Why will it cause tension? A country should be in search for the ideal ways for its own security.”
President Erdogan claimed Greece, a NATO member, had been using Russian-made S-300 systems for years.
He added: “We have now taken steps with Russia about this issue. Deals have been inked. In God’s will, we will see S-400 missiles in our country and precede the process with joint production.
The president also claimed he was unable to negotiate with America over the missile system, which had forced Turkey to see alternative arrangements.
Relations between Nato ally Turkey and the US have deteriorated since a failed coup against president Erdogan in July 2016.
The mutiny was followed by a crackdown by president Erdogan, with an estimated 70,000 alleged opponents of his regime imprisoned.
But Mr Pavel also insisted Turkey remains an internal NATO ally.
Mr Pavel added: “When it comes to democratic deficits, show me one single nation that is perfect. No one is perfect.
“No one challenges the role of Turkey as an important ally at the very difficult crossroads of challenges to the alliance.”