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Chile's president apologised to Israel this week after allowing Palestinian officials to accompany him during a visit to Al-Aqsa Mosque  – a move that sparked outrage in Israel.

Sebastian Pinera, on a visit to Palestine and Israel, toured the Al-Aqsa mosque complex on Tuesday, with images on social media showing him accompanied by Palestinian officials, including Jerusalem affairs minister Fadi al-Hadami.

Israeli officials on Wednesday lashed out at Pinera, claiming his visit was a "violation of regulations" because foreign dignitaries normally coordinate their visits to the volatile site with Israeli officials.

According to Foreign Minister Israel Katz, Chilean Ambassador Rodrigo Fernandez was rebuked for Pinera's visit taking place "in violation of the regulations and a prior agreement".

"The freedom of worship, which Israel observes more than anyone else has, should be separated from safeguarding our sovereignty on the Temple Mount," he said in a Wednesday tweet, using Israel's decription of the site which is considered sacred by Jews and Muslims.

An official source in the Chilean delegation initially hit back at Israel and said the visit was a "private" one, in which "formally, only the delegation from Chile participated".

Later on, Israel's President Reuven Rivlin confirmed Pinera apologised to him for the visit.

The Al-Aqsa compound is located in occupied east Jerusalem and its status is one of the most sensitive issues in the Palestinian-Israeli conflict.

Chile has the largest Palestinian expat population in the world.