The foreign ministry in Damascus said it "condemns the crossing of the Turkey-Syria border by Turkish tanks and armoured vehicles towards the Jarabulus area with air cover from the US-led coalition and considers it a flagrant violation of Syrian sovereignty".
The Syrian opposition in exile, however, welcomed the intervention.
The operation -- named "Euphrates Shield" -- began around 4:00 AM (0100 GMT) with Turkish artillery pounding dozens of targets of the Islamic State (IS) jihadist group around Jarabulus, the Turkish prime minister's office said.
"Syria demands the end of this aggression," the foreign ministry said.
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"Any party conducting a battle against terrorism on Syrian soil must do so in coordination with the Syrian government and the Syrian army who have been fighting this war for five years.
"Chasing out IS and replacing them with terrorist groups backed by Turkey is not fighting terrorism."
Turkish state media later reported that pro-Ankara Syrian rebels had reached the edge of central Jarabulus as part of the Turkey-led operation.
"The Turkish government has abandoned its policy regarding the (Syrian) regime and now finds itself on the same side," it said in a statement.
The Istanbul-based opposition National Coalition, however, hailed the Turkish intervention and stressed that rebel forces were doing the fighting on the ground.
It issued a statement welcoming "the support of Turkey and the international coalition for the military operation in Jarabulus", in which "the rebels are carrying out the combat operations".
Turkey's incursion is its first into Syria since February 2015, when hundreds of Turkish troops crossed the border to move the relics of the grandfather of the founder of the Ottoman Empire.
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