The World Council of Churches will appeal against what it claims is "unjust and discriminatory" action taken against associate general secretary Prof Dr Isabel Apawo Phiri when she arrived in Israel earlier this week.

Dr Phiri, a citizen of Malawi who lives in Geneva, was apprehended at Ben Gurion International Airport on Monday before being interrogated and deported. She had been travelling to attend consultations with church leaders in Jerusalem as part of the Ecumenical Accompaniment Programme in Palestine and Israel (EAPPI). All four other members of the group she was travelling with were allowed entry.

Coordinated by the WCC, the EAPPI programme involves "ecumenical accompaniers" who, according to its website, "offer protective presence to vulnerable communities and monitor and report human rights abuses" and "join Palestinians and Israelis who work in non-violent ways for peace and support the local churches". Almost 1,800 people have taken part in the programme since it was founded in 2002.

A report in the Jerusalem Post this week quoted Israel's Interior Ministry saying Dr Phiri was denied entry due to the WCC's support of EAPPI which it says promotes "anti-Israel activity". "This is actually the first time the State of Israel refuses the entry of a tourist due to a clear background of anti-Israel activity and the promotion of economic, cultural and academic boycotts against Israel," it quoted the Interior Ministry as saying.

It has been alleged Dr Phiri was affiliated with the BDS ("Boycott, Divestment and Sanctions) movement - an argument Rev Dr Olav Fykse Tveit, general secretary of the WCC, told the Post was "built on false conditions, on something that is not true".

In a statement released on Tuesday, Rev Dr Tveit described the accusations made against the WCC and EAPPI programme in the interrogation of Dr Phiri as "completely false" and said he was "very surprised and dismayed that the Israeli Ministry of Interior is apparently basing its decisions on incorrect and unreliable sources".

In the statement, the WCC said it had instructed its legal representatives to immediately appeal the "patently unjust and discriminatory action" taken against Dr Phiri.

Dr Phiri has served as associate general secretary of the WCC, with responsibility for public witness and diakonia, since August, 2012.

EAPPI was established in 2002 after the WCC received an appeal from church leaders in Jerusalem in which they requested the "protection of all people in order to assist the re-establishment of mutual trust and security for Israelis and Palestinians" and called on "all peace-loving people from around the world to come and join us in a manifestation for just peace".