Atalay said that under the accord, the two countries pledged to "prevent the activities of terrorist organisations and primarily the PKK".
The countries committed themselves to the capture and extradition of members of such groups and to prevent them spreading their message through the media.
The separatist PKK is listed as a terrorist organisation by Turkey, the United States and a number of other countries.
It has been accused of using bases in northern Iraq to mount attacks across the border against Turkish targets.
Under a draft provision, which the two countries were unable to finalise, Turkey would be allowed, with prior Iraqi authorisation, to conduct "hot pursuit", or small-scale military operations across the border to hunt down PKK fighters.
Iraqi Kurds, who have been accused by Ankara of tolerating and even aiding the PKK, raised objections to the provision.
The Turkish government has threatened unilateral military action into northern Iraq to attack at PKK bases if Iraq and the US fail to curb the fighters.
On Thursday, Recep Tayyip Erdogan, Turkey's prime minister, urged Washington to act against the PKK, saying that continued inaction was harming US relations with his country.