Iraq's President Abdel Latif Rashid condemned on Tuesday "repeated Turkish attacks", a day after a drone strike on a northern airfield killed three Kurdish counterterrorism officers.
Monday's strike on Arbat airfield, southeast of the city of Sulaimaniyah, also wounded three members of the counterterrorism forces of Iraq's autonomous region of Kurdistan.
"The Turkish ambassador will be called in to receive a letter of protest addressed to the Turkish president", Recep Tayyip Erdogan, Rashid's office said in a statement.
"Mercy be on the martyrs of Iraq, the civilian and military heroes killed by repeated Turkish attacks," the presidency said, after the Patriotic Union of Kurdistan (PUK) in power in Sulaimaniyah had also condemned Monday's "terrorist attack".
Without confirming it was behind the attack, Turkey's foreign ministry on Tuesday accused the regional counterterrorism forces, affiliated with the PUK, of training with "PKK/YPG terrorists" at the time of the explosion.
"This development is quite disturbing as it has clearly revealed the cooperation between PUK's security apparatus and members of the terrorist organisation," it said in a statement.
The ministry said the incident "confirmed once again the accuracy of the measures we have taken regarding Sulaymaniyah".
Fighting between Ankara's army and Kurdish Workers' Party (PKK) militants from Turkey has for decades spilled over into Iraqi Kurdistan, a rugged mountain region where both sides operate military bases.
Ankara also considers the Kurdish People's Protection Units (YPG) in northeast Syria an extension of the PKK, even though it has been backed by the United States as part of an anti-jihadist coalition.
On Sunday, a Turkish drone strike killed a senior official and three PKK fighters in the Sinjar Mountains of northwestern Iraq, Iraqi Kurdish authorities said.
Ankara and its Western allies classify the PKK as a "terrorist" organisation.
- Iraq-Iran agreement -
Turkey operates dozens of military posts in northern Iraq initially established under an agreement struck in the 1980s with the government of executed dictator Saddam Hussein.
In April, Baghdad accused Ankara of carrying out a "bombardment" near Sulaimaniyah airport while US soldiers and the commander of the Syrian Democratic Forces -- a US-backed alliance dominated by the YPG -- were present.
That strike too drew condemnation from the office of president Rashid, who is himself a Kurd.
But Iraqi Kurdistan has for decades hosted several Iranian Kurdish opposition groups hostile to the Islamic republic.
A year ago, Iran repeatedly bombed the groups' positions, accusing them of infiltrating its territory in order to lead attacks against its forces.
Iran also accused them of involvement in protests that exploded after the death in custody of young Iranian Kurdish woman Mahsa Amini.
Tehran set September 19 as a deadline and threatened retaliation if Baghdad failed to implement a "security agreement" which stipulated the disarming of these groups and their settlement in camps far from the Iranian border.
Baghdad said Tuesday it had "respected its commitment" and had transferred these groups "to an area away from the border".
"These groups were disarmed ahead of giving them refugee status," added the statement published by a committee responsible for implementing the agreement, specifying Iraqi federal army border guards were deployed in the recently evacuated border areas.
Asked about the agreement, the UN's Iraq envoy Jeanine Hennis-Plasschaert said "significant progress has been made".
"All sides are genuinely committed to the agreement. Long term security is essential for all," she told AFP.