Iraqi Kurdish officials said Saturday six people had been killed in a pre-dawn strike by Turkish war planes on the village of Zarkel in northern Iraq.
Pro-Kurdish media described the attack as a "massacre" which had left at least nine civilians dead.
The controversy comes after almost a week of intensive bombing by Turkey of PKK targets in the remote mountains of northern Iraq, where the separatist group's military wing is based.
"All the allegations that have been brought forward will be investigated fully," it added, saying a joint study would be conducted with the regional authorities in Iraqi Kurdistan.
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It said the air operation early Saturday was aimed at a camp used by the PKK for logistics and coordination purposes.
All targets during the campaign have been chosen in areas where intelligence shows there are no civilians, the ministry said.
But it also accused the PKK of using "civilians as human shields".
The PKK's insurgency for greater rights and powers for Turkey's Kurdish minority, begun more than 30 years ago, has left tens of thousands dead. A ceasefire declared in 2013 has been shattered by the current violence.