Turkish forces have targeted so-called Islamic State (IS) inside Syria, but have also gone after Kurdish fighters in the same region.
The pursuit of Kurdish forces, whom Ankara considers terrorists, has led to criticism by the United States.
Ankara summoned the US ambassador on Wednesday over comments the foreign ministry called “unacceptable”.
A US military spokesman had expressed hopes on Tuesday that, rather than see Turkey pursue Kurdish fighters, “all parties involved are going to stop shooting at each other and focus” on IS.
“Turkey is a sovereign state, it is a legitimate state,” said EU Affairs Minister Omer Celik, echoing comment by Turkey’s foreign ministry.
“To suggest it is on a par with a terrorist organisation and suggest there are talks between them, that a deal has been reached between them, this is unacceptable.”
Prime Minister Binali Yildirim said on Wednesday that “operations will continue until all terrorist elements have been neutralised, until all threats to our borders, our lands and our citizens are completely over”.
Hurriyet reported that US ambassador John Bass was summoned to the foreign ministry on Wednesday morning.
While Ankara and Washington are allies, the US depends on Kurdish forces for support in attacking IS in northern Syria.
However, Turkey has insisted Kurdish militia, which it regards as terrorists, retreat east across the Euphrates River.
Turkey has been fighting a Kurdish insurgency in its south-east for decades and fears Kurdish gains in northern Syria will fuel Kurdish separatism at home.
Turkish forces and allied factions of the rebel Free Syrian Army (FSA) forced IS out of the Syrian border city of Jarablus a week ago and have since pounded neighbouring villages held by Kurdish-led, US-backed Syria Democratic Forces (SDF).