"A ballistic munition launched from Iran and entering Turkish airspace was neutralised by NATO air and missile defence assets deployed in the eastern Mediterranean," a ministry statement said.

Hours earlier, sirens sounded at Turkey's southern Incirlik airbase, a key NATO facility where US troops are stationed located just outside the southern city of Adana, state news agency Anadolu reported.

NATO air defences shot down a first ballistic missile fired from Iran on March 4, with a second intercepted on Monday.

Adana residents were woken by sirens at 3:25 am (0025 GMT), several posting footage of a fast-moving object in the night sky that appeared to be on fire, the Ekonomim business news website reported.

Defence news site SavunmaSanayiST said they could be "fragments of a third ballistic missile" or of the interceptor, which would have caught fire upon entering the atmosphere.

Iran's embassy in Ankara immediately denied any involvement, saying "no projectile" had been fired towards Turkey, but experts said it was unlikely.

"The first one you can explain it away, the second one possibly, but the third? No. This cannot be accidental," Sinan Ulgen, senior fellow with Carnegie Europe told AFP.

This leaves Ankara in a real bind," he added, saying Turkey would have to find some kind of "low-threshold way to respond".

"In a way, the Gulf countries have not responded but Turkey's political and military culture is different. It's a matter of demonstrating deterrence to Iran, so that things don't escalate further," he said.

- Patience not 'limitless' -

Security sources quoted by local media said Ankara had acted with caution to avoid being drawn into the war.

But one of them also said Turkey did not have limitless patience and wouldn't "hesitate to take the necessary punitive measures".

Monday's incident prompted Washington to close its consulate in Adana and urge all US citizens to leave southeastern Turkey.

Incirlik is an important NATO facility used by US troops for decades. It also hosts military personnel from Spain and Poland, its website says.

Experts say it also houses 50-60 US-owned tactical nuclear weapons.

US troops are stationed at Kurecik base in Malatya where they man an early-warning radar system NATO describes as a "key element" of its missile shield that can detect Iranian missile launches.

Although Ankara has categorically denied radar data has ever been used to help Israel, its presence has rattled Tehran.

On Tuesday, Turkey said a Patriot missile defence system was being deployed in Malatya just days after NATO moved to strengthen its "alliance-wide ballistic missile defence posture".

Just hours before the third missile was intercepted, Turkey's transport minister said a Turkish-owned ship had crossed the Strait of Hormuz with Iran's permission, without saying when.

The crucial shipping route has been almost totally closed to traffic since the war began.