His Most Godly Beatitude Theophilus III, who is touring the UK said that rules protecting the rights of Jews and Christians to live together and access holy places, are being undermined.
In a statement recorded at Premier, he explained what had prompted his visit.
He said: "We have been mandated by all the church leaders in the holy land to share our story and raise awareness of the challenges we are facing as a Christian community in Jerusalem.
"Recently we have seen the emergence of a trend that threatens to undermine the Christian presence and destabilise the peace of the holy city of Jerusalem.
"The 'status quo' rules, that has guaranteed the rights of Jews, Christians and Muslims to live, flourish and thrive together in Jerusalem for centuries is in grave danger. This code, that has safeguarded our religious freedoms and provided access to the most holy places for all people, is being dangerously undermined."
He said members of the national legislature of Israel (Knesset), last July signed a proposed bill for debate in the Israeli parliament, which if passed, will severely restrict the rights of the Churches to deal freely and independently with their lands. He added that it could also lead to their land being confiscated.
Spokesperson for the Patriarch, ambassador Partick Theros, told Premier's News Hour how bad the situation for Christians in Jerusalem is.
He said: "In the last couple of decades, a small but very vociferous and very well connected settler movement has grown in strength and they are clearly bent on reducing the non-Jewish presence - especially in the old city of Jerusalem."
Their shared concerns come as many people around the world mark the centenary of the Balfour declaration, which was when the British Government announced their support for the establishment of a "national home for the Jewish people" in Palestine.
"We should remember however that the same declaration said without prejudicing the rights of the other people living in Palestine as well as not prejudicing the rights of various different religious institutions, which is fairly explicit.
"So the Balfour declaration is a perfectly valid document in the relationship between Britain and Israel but it's the entire declaration we should look at."
The Patriarch of Jerusalem has met with Heads of State, the Pope and the Archbishop of Canterbury to warn them that "if we do not act soon it will be too late. And the outcome will be catastrophic".
He told Premier why he has decided to bring the issue to the world's attention.
He said: "Before, we stood silent, bearing patient witness to a harsh campaign against us and against our church.
"Every day we face false accusations, suspicion and slander. Our detractors target our heritage and our integrity. Today, Our calling and commitment to the Lord means we can accept this no longer and this has lead us to break our silence and simply say, 'enough is enough.'"
This bill is an assault on the freedom and independence of our Churches which have served and supported Christians in the Holy Land for two millennia. Were it to be passed, this bill would be in clear violation of the "Status Quo" and arguably, numerous international treaties."
Listen to ambassador Partick Theros sepaking with Premier's Tola Mbakwe: