A military statement said the air strikes targeted the Zap region, the Turkish name for a river which flows across the Turkish-Iraqi border and is known as Zab in Iraq.
The air strikes hit "two hiding places and one shelter, and killed six separatist terrorist organisation militants who were understood to be preparing an attack," the statement said.
The raids were part of a widening campaign against the outlawed Kurdistan Workers Party (PKK) which has also hit other Kurdish fighters inside Iraq - apparently by accident.
On Tuesday, Turkish planes bombed Kurdish targets in Iraq's Sinjar region and northeast Syria, killing about 70 militants inside the two neighbouring states, according to a Turkish military statement.
The United States expressed "deep concern" over those air strikes and said they were not authorized by the US-led coalition fighting Islamic State.
The Syrian foreign ministry on Wednesday condemned the Turkish strikes as an act of aggression and warned against infringing Syria's territorial sovereignty.
Five members of the Iraqi Kurdish Peshmerga forces, which are also deployed in Sinjar, were killed. Kurdish authorities who run their own autonomous region in north Iraq enjoy good relation with Turkey and, like Ankara, oppose the presence of a PKK affiliate in Sinjar.
Turkish President Tayyip Erdogan on Tuesday told Reuters that he would not allow Sinjar to become a PKK base, adding that Ankara informed its partners including the United States, Russia and Iraqi Kurdish authorities ahead of the operation.
On Wednesday, Turkish foreign ministry spokesman Huseyin Muftuoglu said the parties were informed through both military and diplomatic channels.
Turkey had passed on information to the United States and Russian military attaches in Ankara, Muftuoglu said, and Turkish army chief Hulusi Akar also held a telephone conversation with his US and Russian counterparts.
The Combined Air Operations Center in Qatar, responsible for providing command and air control in regions including Iraq and Syria, was also informed in advance, Muftuoglu said.
Designated a terrorist group by Turkey, the United States and the European Union, the PKK has waged a three-decade insurgency against the Turkish state for Kurdish autonomy. More than 40,000 people have been killed in the conflict, most of them Kurds.
The Turkish army also reported on Wednesday cross-border mortar fire from two areas inside Syria -- one believed to be under the control of Syrian government forces and the other by Kurdish YPG militants. It said there were no casualties, and it retaliated.
YPG spokesman Redur Xelil said there was heavy Turkish artillery fire across the border into Syria on Wednesday. The shelling hit near Darbasiya, a town in a Kurdish-controlled part of northeast Syria.
The Syrian Observatory for Human Rights war monitor reported clashes between Kurdish fighters and Turkish forces along the border near Darbasiya.
Kurdish women carry flags as they protest, in the northeastern city of Qamishli, against Turkish airstrikes on the headquarters of the Kurdish fighters from the People's Protection Units (YPG) in Mount Karachok on Tuesday.
Turkish warplanes hit Kurdish militant targets in northern Iraq on Wednesday and killed six militants, the military said, in a second day of cross-border raids.
