It marks the second ballistic missile Iran has fired over the NATO member in the space of a week.
“We once again emphasise that all necessary steps will be taken resolutely and without hesitation against any threat directed at our country’s territory and airspace,” Turkey’s defence ministry said.
Earlier, the US suspended its consular services in southern Turkey and ordered non-essential staff to leave.
Debris from the munition reportedly landed in the Gaziantep province in southern Turkey, around 150 kilometers (93 miles) from the Incirlik Air Base.
The Incirlik base is used by foreign military forces, including the US and other NATO allies. It is controlled by the Turkish air force but operates as a joint Turkish-US airbase.
Turkey became the first member of the NATO alliance to have been drawn into the expanding Middle East conflict after the Iran fired its first missile towards the country on Wednesday.
On Saturday, Ankara warned Iran against launching another attack. But Tehran denies firing the missile.
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NATO chief Mark Rutte raced to confirm Article 5 was not on the table as fears surged other members could be dragged into the war.
Article 5 rules that an armed attack on one NATO ally is considered an attack on all members – and deems that all members of the alliance will do what is necessary to assist the targeted country.
Meanwhile, the UK’ s RAF Akrotiri base in Cyprus was hit by an Iranian drone last Monday.
Greece, Turkey, France and the UK have dispatched jets and warships to the Mediterranean island in response.
Speaking on Monday, French President Emmanuel Macron said: “When Cyprus is attacked, it is Europe that is attacked.
“The defence of Cyprus is obviously a key issue for your country, for your neighbour, partner and friend, Greece, but also for France and, with it, the European Union.”
Mr Macron is in Paphos today to meet leaders of Cyprus and Greece for discussions on collective security and de-escalation in the conflict.
However, Iran’s Foreign Ministry has denied launching the drone attack on RAF Akrotiri.
Spokesperson Esmaeil Baghaei said that strikes on Turkey, Cyprus and Azerbaijan did not originate in Iran.
“No offensives were initiated from Iranian territory,” he said.
Baghaei also suggested that some of the attacks were “staged”.
“We have warned repeatedly that the enemy may stage certain attacks to drive a wedge between us and other countries,” he said.
Speaking to LBC on Monday, former Defence Secretary Ben Wallace likened Sir Keir Starmer’s response to the attack on the British base to “a rabbit in the headlights”.
“I think the spectacle we see at the moment, which was Keir Starmer saying on Saturday, you can’t use my bases, on Sunday, you can, just made us look ridiculous. “And we saw the United States asking to use our bases in order to do certain military actions to protect British citizens, both in Dubai, the Gulf, the wider Gulf, and indeed in Cyprus, while we were saying no to them, I mean, that was ridiculous,” he told LBC.