Police used pepper gas and batons against up to 1,000 Turkish ultra-nationalists on Sunday protesting against Patriarch Bartholomew, the Istanbul-based head of the world's Orthodox Christians.
Ultra-nationalists in overwhelmingly Muslim Turkey oppose allowing the Greek Orthodox church to own land and have been upset by reports the government wants to reopen an Orthodox seminary on the island of Heybeliada near Istanbul.
The demonstrators, chanting slogans and waving nationalist banners, hung an effigy of the patriarch on a tree and set it alight. Their protests were also aimed at the increasing number of foreigners buying property in Turkey.
The demonstrators clashed with police after being prevented from marching on the church beside the Bosphorus in the Fener district of Istanbul, which also houses the patriarch's offices.
Turkish television said police detained a number of protesters.
The Halki seminary is a sensitive issue in Turkey, which has enacted a flurry of political reforms in its drive to persuade the European Union in December to open entry talks. EU member state Greece has long called for the seminary to be reopened.
Patriarch Bartholomew recently complained in an interview to Reuters that his church continued to face legal and administrative obstacles despite the government reforms.
Istanbul, then known as Constantinople, was the centre of Orthodox Christianity until it fell to the Muslim Ottoman Turks in 1453. The patriarch remains nominal head of the church, though the number of Orthodox Christians in Turkey is now tiny.
Religious freedom is expected to be high on the agenda of EU Enlargement Commissioner Guenter Verheugen, who arrives in Turkey on Sunday evening for four days of talks ahead of next month's crucial progress report on Ankara's readiness for negotiations.