Turkey says Syria fired on one of its planes that was taking part in a rescue operation for a warplane shot down by Syrian forces last Friday.
Turkey's deputy PM said the CASA search and rescue plane, looking for the F-4 Phantom jet, was not brought down.
He vowed Syria would "not go unpunished" but that Turkey had "no intention" of going to war.
Nato will discuss the downing of the jet on Tuesday at a meeting called by Turkey, a member state.
Speaking at a televised news conference, Turkish Deputy Prime Minister Bulent Arinc did not specify when the second incident took place and did not say whether the search and rescue plane was hit.
He said the Syrians had stopped firing following a warning from the Turkish side.
Mr Arinc said Turkey would protect itself within the framework of international law, but had "no intention of going to war with anyone".
Syria has insisted the F-4 was engaged while it was inside its airspace.
Syrian foreign ministry spokesman Jihad Makdissi said the location of the wreckage would prove its case.
He said on state TV: "There is no doubt that the Syrians intentionally shot down our plane in international airspace. The facts in our possession show that our plane was hit by a heat-seeking laser-guided missile."
He added: "To target an aircraft in this fashion without any warning is a hostile act of the highest order."
Mr Arinc also said Turkey would decide in the coming days whether to cut electricity exports to Syria, a move he said had not yet been taken because of "humanitarian reasons".
Turkey has also sent a letter to the UN Security Council saying the downing of its jet poses a serious threat to peace and security in the region.
The BBC's Barbara Plett at the UN says the letter does not ask the council to take any action.
A senior Western official at the UN said he did not expect a military response from either Ankara or Nato.
Meanwhile, the search is continuing for the jet and its crew, but hopes of the two men being found alive are fading.
Nato members have condemned Syria's actions and convened a meeting under article 4 of its constitution, which states any member can request talks if it feels its territorial integrity has been threatened.
The BBC's Jonathan Head in Istanbul says Turkey is looking for the strongest possible diplomatic support from its allies over the incident - but its options for showing its anger to Syria are very limited.
On Monday, EU foreign policy chief Catherine Ashton urged Turkey to be "restrained in its response".
German Foreign Minister Guido Westerwelle also urged calm, saying: "De-escalation is crucial at this moment."
Trickle of defections
Earlier on Monday, Turkish media reported that several high-ranking Syrian military figures had defected to Turkey.
A general, two colonels, two majors and about 30 other soldiers were said to have crossed into Hatay province on Sunday night.
They were part of a group of some 200 people who crossed the border, the Anatolia news agency said.
There has been a steady trickle of defections from the Syrian armed forces over the past year, most of them to opposition forces fighting inside the country.
Our correspondent says this is one of the biggest single groups of soldiers to defect to Turkey but so far there is no evidence that they have had a significant impact on the Syrian military's ability to fight.