Ilnur Cevik said in a radio interview with Turkish media on Wednesday that US military vehicles patrolling the border with their Kurdish allies were at risk of coming under fire, local media reported.
Turkey last week bombed targets of the Kurdish Peoples' Protection Units [YPG] in Syria, earning the wrath of its NATO ally Washington.
"If PKK terrorists keep up their actions inside Turkey… as you know they are infiltrating from northern Syria," Cevik said, referring to the outlawed Kurdistan Workers' Party [PKK].
"If they go too far, we won't care about the US armoured vehicles and maybe some rockets will hit them by accident," he added.
Ankara has deemed the YPG a terror organisation and the Syrian branch of the PKK, which has waged an insurgency since 1984 inside Turkey that has left tens of thousands dead.
Cevik was, however, quick to issue a clarification on his comments.
"Turkey has never and will never hit its allies anywhere and that includes the US in Syria," he tweeted on the same day.
The top adviser insisted however that US troops were "shielding terrorists" in Syria in a move that was "alienating the Turkish people".
Pentagon spokesman Eric Pahon slammed the comments as "irresponsible and unacceptable", stressing that Turkey and Syrian Kurdish forces were America's "most trusted allies in the fight against the Islamic State group".
The YPG has been seen by the US as the best ally on the ground in the fight against IS extremists in Syria and Trump has inherited a policy from Barack Obama of actively supporting the group.
The US has backed the formation of the Syrian Democratic Forces [SDF], dominated by the YPG but also including Arab fighters, yet Ankara contends it is merely a front for the Kurdish group.
Last week, Turkish President Recep Tayyip Erdogan said Ankara was "seriously saddened" by footage showing US military vehicles operating close to the border with YPG forces.
Washington has sent military vehicles with US flags to the Syrian side of the frontier accompanied by YPG fighters to carry out patrols, in an apparent bid to prevent further fighting.
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