The statement came a day after Turkish Parliament voted in favor of the deployment of cross-border troops to Iraq and Syria to fight ISIS and other terrorist organizations.
The ministry said the "declared policy of the Turkish government represents a real aggression against a member state of the United Nations."
The motion is not limited to ISIS but includes a range of threats to Turkey's national security and was combined with another motion on the deployment of Turkish forces in northern Iraq to fight the Kurdish separatist terror group PKK. That measure allows military incursions into Syria and Iraq against a threat to Turkey and allows foreign forces to use Turkish territory for possible operations against ISIS.