The World Council of Churches has said it "deeply regrets" a decision by Israel to refuse entry to a woman on the grounds that she was working against the interests of the state.
Dr Isabel Phiri, from Malawi, was turned back at Ben Gurion airport on Monday.
According to Breaking Israel News, this sets a precedent which could see thousands of activists denied entry in future.
The refusal to admit her came a few months after Israel's interior minister Aryeh Dery and public security minister Gilad Erdan announced plans to deny entry to Israel to advocates of the boycott, divestment and sanctions movement (BDS) movement and to deport anyone already there.
Phiri was travelling to Israel to take part in consultations in Jerusalem on the Ecumenical Accompaniment Programme in Palestine and Israel (EAPPI), which is a programme of the World Council of Churches.
Israeli officials believe the EAPPI programme is anti-Israel.
Dery told Breaking Israel News: "Granting an entry permit to activists such as Phri would in effect reinforce the wrongful activities she and her peers are advancing and I have no intention of lending a hand to that.
"I will use any authority at my disposal to avert harm to Israel.
"The place of the boycotters is outside the country's borders and we shall continue to do everything possible to prevent them from entering our country."
The WCC, which has lodged an appeal, said it "deeply regrets the Israeli antagonism against the WCC's initiatives for peace with justice for both Palestinians and Israelis".
The WCC noted that Phiri was the only African member of the WCC staff delegation and the only one denied entry.
The reason given for her deportation was "prevention of illegal immigration considerations".
WCC general secretary Dr Olav Fykse Tveit said: "The accusations made against the WCC and the EAPPI programme in the interrogation of Dr Phiri and published in the media today are completely false.
"I am very surprised and dismayed that the Israeli Ministry of Interior is apparently basing its decisions on incorrect and unreliable sources."
The EAPPI programme was set up in response to an appeal from church leaders in Jerusalem in 2002.
They wrote in a letter: "We would respectfully request protection of all people in order to assist the re-establishment of mutual trust and security for Israelis and Palestinians. Further, we would call on all peace-loving people from around the world to come and join us in a manifestation for just peace".
More than 70 churches, ecumenical bodies and specialised ministries in 22 countries from Africa, Asia, Europe, North America and Latin America actively participate in the programme. Almost 1,800 "accompaniers" have taken part, travelling to the West Bank to monitor and help local communities.
Earlier this year, several WCC staff and other representatives were detained by security staff at Ben Gurion airport.
The Church of England officially has supported EAPPI. In 2012, General Synod passed a motion "encouraging parishioners to volunteer for the programme and asking churches and synods to make use of the experience of returning participants." A few months later, the new Archbishop of Canterbury Justin Welby expressed regret at his support for the motion which on reflection he felt did not "adequately reflect the complexity" of life on the ground in Israel. He said he would have been happy to have supported the motion if it had stated that Israel had the right to "live in security and peace within internationally agreed borders, and the people of the region have the right to justice, peace, and security, whoever they are."
Christian Today has asked the Israeli Embassy in London for comment.
