Iraqi president’s comments come as Turkish counterpart makes first trip to Baghdad.
The military said that operations would continue in the area.
The Kurdish group is listed as a “terrorist” organisation by the government in Ankara, as well as the United States.
The clashes came as Besir Atalya, the Turkish foreign minister, arrived in Baghdad for discussions on joint efforts to tackle the PKK.
“We expect both the central Iraqi government and the regional administration in the north to undertake concrete steps,” he said before departing.
The talks in the Iraqi capital are part of three-way consultations between Turkey, Iraq and the US, initiated last year, Turkey’s Anatolia news agency quoted Atalay as saying.
He said he hoped the co-operation would “produce good results, particularly in intelligence sharing”.
During a visit to Baghdad by Abdullah Gul, the Turkish president, last month, Jalal Talabani, his Iraqi counterpart and a Kurd, said the PKK must lay down its arms or leave the country.