Hoshyar Zebari said: "There will be closer cooperation between Baghdad and the regional Kurdistan government to work together and flush out these foreign fighters."
He did not give details about the cooperation between the two forces. The Kurdish Peshmerga have long been a force in the jockeying between Shi'ites, Kurds and Sunnis for influence and control of northern Iraqi oilfields.
Describing the fall of Mosul as "dramatic", Mr Zebari called on all Iraqi leaders to come together to face the "serious, mortal" threat to the country. Speaking in Athens, he added: "The response has to be soon. You cannot leave these people to stay there to entrench themselves for a long time."
His comments were made before it emerged militants had also seized control of Saddam Hussein's home town of Tikrit, 80 miles north of Baghdad
Militants also seized the Turkish consulate in Mosul and efforts were made to ensure the safety of diplomatic staff.
The seizure of the consulate comes a day after 28 Turkish truck drivers were abducted by militants while delivering diesel to a power plant in the city.
Earlier, security sources said militants from the Islamic State in Iraq and the Levant (ISIL), an offshoot of al Qaeda, had advanced into the oil refinery town of Baiji, setting the courthouse and police station on fire. Guards were allowed to leave.