Turkey and Iran presented a united front in their opposition to Iraqi Kurdish aspirations of independence, during a visit Wednesday by Turkish President Recep Tayyip Erdogan that signals a warming of ties.
Ayatollah Khamenei further termed the development as an "incident", adding that Iran and Turkey must take any possible measures to confront with the incident.
Iran and Turkey have already threatened to join Baghdad in imposing economic sanctions on Iraqi Kurdistan and have launched joint military exercises with Iraqi troops on their borders with the separatist region.
"The political, economic and global relations between Iran and Turkey are in a good position, but we should strive to advance military and defense cooperation consistent with other fields", Iranian President Hassan Rouhani said Tuesday after his meeting with the Turkish top general.
Turkish armed forces chief of staff General Hulusi Akar also came to visit the Iranian capital on Sunday.
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"We regard the secessionist move in Iraq as detrimental to security of the region", Hatami said on Tuesday.
Turkey, a country with a Sunni majority, and Shiite Iran have been on opposite sides of the conflict in Syria, as Tehran supports Syrian President Bashar al-Assad's government while Ankara has been seeking to topple him.
Before the press conference, Erdogan and Rouhani co-chaired the fourth meeting of Turkey-Iran High-Level Cooperation Council, which led to four cooperation documents on banking and customs, among other fields. The two countries have held military manoeuvres close to their borders with Iraq's autonomous Kurdish region in recent days to ratchet up the pressure on Kurdish leaders.
"The referendum in Kurdistan was against the Iraqi constitution, which does not help the people of Kurdistan, and is not justifiable for Iraq's security", Mohammad Javad Zarif said.
Erdogan was accompanied by a high-ranking delegation comprising ministers of economy, energy, customs and culture, as well as Turkish investors and business leaders.
The independence referendum was opposed by many countries because it would threaten the integrity of Iraq and it could undermine fight against Islamic State militants.