Ahmet Mete, the elected mufti of Xanthi (Iskeçe) in Greece's Western Thrace region, died at the age of 57 on Thursday, the Muslim official's family said.
The family did not mention the cause of death but Mete had been suffering from cancer for several years.
President Recep Tayyip Erdoğan reacted to the news in a tweet, writing in Turkish: “I wish God’s mercy on Ahmet Mete Hocaefendi, the Elected Mufti of Xanthi. I convey my condolences to the family (and) loved ones of our deceased teacher and to all my brothers and sisters living in Western Thrace.”
Foreign Minister Mevlüt Çavuşoğlu hailed Mete as a person who "devoted his life to the just struggle of the Western Thrace Turkish minority."
"His services will always be remembered fondly," he said on Twitter.
Turkish Parliament Speaker Mustafa Şentop also expressed "great sadness" over Mete's death.
Born in 1965 in Yanioren, a village in Xanthi, Mete studied in Turkey and Saudi Arabia at undergraduate and graduate schools before returning to Western Thrace.
He served as a Quran teacher and imam under the region's former mufti, Mehmet Emin Ağa.
Western Thrace is home to a Muslim Turkish minority of around 150,000 people, where muftis, who are Muslim scholars and legal experts, have legal jurisdiction to decide on family and inheritance matters in the local community.
The Muslim minority is multiethnic, made up of Turks, Bulgarian-speaking Pomaks and Roma, and all were long discriminated against by the Greek state, including restricting movement.
The election of muftis by Muslims in Greece was regulated in the 1913 Treaty of Athens with the Ottoman Empire and was later included in Greek law. Greece, however, annulled the law in 1991 and started appointing muftis itself.
The majority of Muslim Turks in the cities of Komotini (Gümülcine) and Xanthi do not recognize the appointed muftis and instead elect their own, who are not recognized by the Greek state.
Turkey has long decried Greek violations of the rights of Muslims and the Turkish minority, from closing mosques and shutting schools to not letting Muslim Turks elect their religious leaders.
The measures violate the 1923 Treaty of Lausanne as well as European Court of Human Rights (ECtHR) verdicts, making Greece a state that flouts the law, Turkish officials say.