"We should not allow terrorist organisations, in particular the PKK, to weaken our relations," he said.
The PKK hideouts in the mountains on the Iraqi side of the border were at the centre of the talks.
Around 40,000 people have been killed in fighting between the PKK and the Turkish military since 1984, when the PKK took up arms with the aim of establishing an ethnic homeland in southeast Turkey.
Turkey, the European Union and the US view the PKK as a terrorist organisation.
Air raids intensified
Turkey's military has boosted air raids in the region in recent weeks.
Ankara has accused the Iraqi Kurds, who run an autonomous administration in northern Iraq, of tolerating and even aiding the PKK.
Jalal Talabani, the Iraqi president, who is a Kurd, said on Wednesday that both Baghdad and the Kurdish administration in northern Iraq were determined to purge the region of the PKK.
"We, the Iraqi Kurds, will no longer allow armed people from any Kurdish group to use our territory to carry out attacks on Turkey or Iran," he said in an interview with Turkey's Aksam daily.
He said Kurdish parties in northern Iraq would soon convene a meeting to issue a joint appeal to the PKK to abandon its armed struggle.