"There will be closer cooperation between Baghdad and the regional Kurdistan government to work together and flush out these foreign fighters," Hoshyar Zebari said on the sidelines of a EU-Arab League meeting in Athens.
He did not give details about the cooperation between the two forces.
Describing the fall of Mosul as "dramatic", Zebari called on all Iraqi leaders to come together to face the "serious, mortal" threat to the country, Reuters reported.
"The response has to be soon," he said. "You cannot leave these people to stay there to entrench themselves for a long time."
Earlier on Wednesday, security sources said militants from the Islamic State in Iraq and the Levant (ISIL), an offshoot of al Qaeda, advanced into the oil refinery town of Baiji, setting the courthouse and police station on fire.