Theophilos III has been sworn in as the patriarch of the Greek Orthodox Church in Jerusalem, in a ceremony at the Church of the Holy Sepulchre.
Israel objected to the swearing in of Theophilos III
The patriarch is the religious leader of 100,000 Christians in the Holy Land.
The ceremony was held despite the fact that the Israeli government has not yet recognised him as patriarch, and is actively supporting his predecessor.
Irineos I was demoted to a monk after being accused of selling church land in East Jerusalem to Jewish investors.
The sale sparked outrage among Palestinians who opposed any strengthening of a Jewish presence in East Jerusalem, which they hope will become the future capital of a Palestinian state.
Irineos has refused to recognise his dismissal by the Orthodox Church in June.
Israel delays approval
The Palestinian Authority and Jordan have backed the church's decision, but Israel has delayed giving its approval.
Israel's minister in charge of Jerusalem affairs in the prime minister's office, Tzachi Hanegbi, earlier this month warned the patriarchate not to inaugurate Theophilos III.
Irineos refused to recognise his dismissal
"The state objects to holding this ceremony, which is intended to validate the removal of Patriarch Irineos, a move that has not been recognised by the State of Israel, as is required by law," he said in a letter obtained by Israeli newspaper Haaretz.
Mr Hanegbi said that his government planned to appoint a committee to deal with the matter and that Theophilos would only be able to claim the patriarchate after it had made its decision.
The patriarchate replied angrily to Mr Hanegbi's demand.
"With all due respect, the Patriarch, the Synod and the Patriarchate find your letter surprising and unacceptable since it constitutes an outright and inappropriate interference in their autonomy as a religious sect and in the religious freedom of members of the Greek Orthodox congregation," it said.
"There is no need and no place for a 'ministerial committee', whether ordinary or special, and it is fitting for the government to hurry up and recognize the patriarch, unless it is indeed extraneous and improper considerations that are guiding you."
Theophilos III, originally from Messini in Greece, was elected the 140th Patriarch of Jerusalem and all Palestine on 22 August.
He served previously as Archbishop of Tabor in the Czech Republic.