Foreign Minister Hakan Fidan said any effort to stir up a civil war inside Iran in a bid to bring about regime change would be a "historic" mistake.
"We are against all scenarios that aim to instigate a civil war in Iran, that target ethnic or religious fault lines," Fidan told journalists in Istanbul.
"This is the most dangerous scenario," he added.
He was speaking after reports that Washington was looking to arm Kurdish guerrillas to infiltrate Iran, with US President Donald Trump expressing support for such an offensive.
However Trump said Saturday that "We're not looking to the Kurds going in".
"We're very friendly with the Kurds, as you know, but we don't want to make the war any more complex than it already is," he told reporters in a briefing aboard Air Force One.
Fidan said he had raised the matter with US Secretary of State Marco Rubio, who had denied any American involvement in such an issue.
"They stated they are not involved in such an effort and have no such intention," Fidan said after the pair spoke on Wednesday.
He pointed the finger instead at Israel's "strategy of using Kurdish groups in the region as proxies".
Such a move would raise hackles in Turkey, which has fought a decades-long bloody conflict with the Kurdish militant group PKK, which it is now seeking to end.
"We are openly warning everyone... against this scenario," Fidan said.
"This will not only lead to more suffering and loss of life for innocent civilians in Iran, but it will also cause millions to be displaced and flee to neighbouring countries and beyond."
"After Iraq and Syria, a long period of uncertainty, war and turmoil in Iran is not in anyone's interest," he added.
"Any internal crisis there would have a ripple effect spreading throughout the region. That's why we're trying to stop it."
- 'Be careful' -
Fidan also issued a warning to Tehran after NATO intercepted a ballistic missile launched from Iran heading towards Turkey on Wednesday.
"We are not a country that is easily provoked," Fidan said.
"We spoke with our friends in Iran and said if this was a missile that lost its way, that's one thing.
"But if this is going to continue... our advice is: be careful, don't let anyone in Iran embark on such an adventure," he said.
Spanish Defence Minister Margareta Robles on Thursday said the missile had been spotted by Spanish troops manning a Patriot missile battery at the Incirlik air base, a key NATO facility in southern Turkey.
They had "detected and reported the missile attack", she said, though they were not the ones that shot it down.
NATO "condemned Iran's targeting of Turkiye" and said it had strengthened its "ballistic missile defence posture" as Iran stepped up its strikes across the Middle East in retaliation for the US-Israeli strikes.
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