Pope Tawadros II has arrived in Jerusalem in a historic visit that marks the first time that a head of the Egyptian Coptic Orthodox Church has visited the city since Israel's occupation of East Jerusalem in 1967.

The website of the Coptic Church in Jerusalem said the pope's only reason for the visit on Thursday was to attend the funeral prayer of the Bishop of Jerusalem Anba Abraham, the head of the Coptic Church in the Holy Land, who died on Wednesday.

The late Egyptian Pope Shenouda III had issued a ban in 1979, in the aftermath of the Camp David peace accords between Egypt and Israel, preventing Egyptian Coptics from pilgrimage to Jerusalem while under Israeli occupation.

Father Boules Halim, the spokesman for the Coptic Church in Cairo, said that the visit was arranged for an "exceptional situation".

Halim told the AFP news agency that the visit will not change the stance of the Egyptian Church towards the occupation which it historically opposes.

"The stance of the Coptic Orthodox Church concerning travelling to the Holy Lands will always remain the same. The Pope's visit came as an exception," said Halim.

"The position of the church remains unchanged, which is not going to Jerusalem without all our Egyptian [Muslim] brothers."

The Egyptian government does not ban Egyptian citizens from visiting Israel and encourages normal relations between the two countries.

Shenouda III, who was head of the Egyptian Coptic Church for more than 40 years, until his death in 2012, was against normalising relations with Israel despite the peace treaty between the two countries.