The U.S. ambassador to NATO told CNBC that Turkey's purchase of a Russian missile system could help the Kremlin in its bid to weaken NATO.

Turkish officials reportedly have until the end of this week to cancel the purchase of Russia's S-400 missile defense system and instead buy Raytheon's U.S.-made Patriot missile.

U.S. officials see Ankara's purchase of the missile system as a pivot toward warmer ties with Moscow. Turkey's integration of the Russian S-400 system is viewed as a direct threat to the security of Lockheed Martin's F-35 fighter jet program which Turkey is a part of.

Kay Bailey Hutchison, the U.S. NATO ambassador and former U.S. senator, told CNBC's Hadley Gamble Tuesday that Russia is trying to "continue to probe ways" to disrupt and weaken the NATO alliance, adding that a Russian missile system under the same military control as an F-35 fighter jet was unacceptable.

"You have to make a choice. You can have one or the other but not both," she said, before repeating that Turkey stands to "lose association" with the F-35s that they have already ordered.

If Turkey refuses to comply with Washington's demands, it faces losing their supply chain position within the F-35 program. In April, Turkish President Recep Tayyip Erdogan claimed the U.S. jet program would collapse without Turkey's input.

In late May, the Turkish lira saw a rare move higher after President Donald Trump spoke with Erdogan via telephone and set up a late June meeting. The currency had shed around 14% year-to-date amid the friction between the NATO allies.