"Let me openly say that there are some willing to start a regional Cold War," Foreign Minister Ahmet Davutoglu told state-run Anatolian news agency.
"We are determined to prevent a regional Cold War.
Sectarian regional tensions would be suicide for the whole region," he warned.
Tension has grown between Sunni powerhouse Saudi Arabia and Shiite Iran.
Gulf Arab countries are concerned over Iran's controversial nuclear program, which the West accuses Tehran of masking it for nuclear weapons.
Tehran says its program only aims to generate electricity.
Iran has faced accusations of sparking unrest in Shiite-majority Bahrain last year, which prompted Saudi Arabia to send troops to help stabilize the tiny Gulf country.
Tension has sharply grown between the two rivals after the US accused Iran of plotting to kill the Saudi ambassador in Washington, a claim denied by Tehran.
"Turkey is fiercely against new regional Shiite-Sunni tensions, or an anti-Iran or similar tensions arising like in the Gulf," said Davutoglu, who arrived in Tehran on Thursday for talks on Iran's nuclear program.
Tension has also grown between the West and Iran after an Iranian threat to shut the Strait of Hormuz, a critical route for oil transfer, if the West imposed new sanctions over its nuclear program.
The top Turkish diplomat singled out the case of neighboring Iraq, which is splitting up into sectarian and ethnic fiefdoms.
"Our Iraq policy foresees close contact with all sides, Davutoglu said.
Sectarian tension has grown in Iraq following the 2003 US invasion to topple the Saddam Hussein regime, claiming thousands of lives.
Following the US invasion, the Kurds consolidated their autonomy in the north, Shiites dominated across the south and Baghdad, and Sunnis are exploring whether to set up their own autonomous region in the centre and west.
Tension has escalated after Prime Minister Nouri Al-Maliki, Shiite, issues an arrest warrant against Sunni Vice-President Tareq Al-Hashimi.
At least 24 people were killed Thursday after two bomb explosions rocked Shiite areas in Baghdad.
No one should make a mistake here, Davotoglu said.
Sunni-majority Turkey is worried that Iran's growing influence in Iraq could result in escalating tension among Iraqi sects, resulting in the country's partition.
No one should act with a conviction that one ideology, one sect, one ethnicity could dominate in any country as it was the case in the past. The societies in the region want a new political understanding."
Tehran has criticized Ankara for siding with the West against Syrian President Bashar Al-Assad, who is facing popular protests to quit power.
We have different opinions on Syria but our stance has principles. They have their own perspectives and principles. We may discuss them, Davutoglu said.Everybody in this region is a friend and brother. If Bashar al-Assad had not launched this war against his own people, we would not be facing such a problem.
Reproduced with permission from OnIslam.net