The president of Chile refused to accept the credentials of Israel's new ambassador on Thursday in a move that Israel says "seriously harms relations".

Ambassador Gil Artzyeli was scheduled to meet President Gabriel Boric at his residence in Santiago on Thursday to be formally accepted as Israel's new representative, but the president refused to see him, reportedly citing Israel "killing children in Gaza".

Artzyeli had already arrived at the president's residence when he was informed that the president would not accept his credentials, but the new ambassador told reporters afterwards that senior Chilean foreign ministry officials “apologised multiple times” to him personally and the State of Israel.

In a statement on Friday, Israel's Ministry of Foreign Affair slammed the "puzzling and unprecedented behaviour of Chile", adding that it has summoned the South American country's ambassador on Sunday where Israel's response will be detailed.

GettyImages-1237355266 Gabriel Boric

Gabriel Boric, the 35-year-old President-elect of Chile (Getty Images)

After being told that the president refused to see him, Ambassador Artzyeli told reporters: "Regarding the reason for the cancellation of the appointment, the death of a minor in the West Bank, in the Middle East there is a conflict that has lasted for 100 years, and there are victims on both sides. The new Middle East is in an era of peace."

"For me, it was a rather awkward incident this morning, but being an Israeli and a Jew, my people have been through worse in the last 4,000 years."

He said that Chilean Foreign Minister, Antonia Urgula, and another senior official apologised profusely for the incident: "I was invited by the minister and we had a long meeting of more than an hour in which they repeatedly apologised to me and to the State of Israel.

"We are going to overcome the incident for the benefit of Chile, Israel and our bilateral relations. I have received the apology and we are turning the page," he added.

A Chilean diplomat told the local media: "There is now a huge commotion in the government and the foreign ministry, we need to see how to fix this problem."

According to Israeli media, military personnel killed a 17-year-old Palestinian during clashes with gunmen in the West Bank overnight.

In a statement, Israel's Ministry of Foreign Affairs said: "Israel views with severity the puzzling and unprecedented behaviour of Chile. This seriously harms relations between the countries.

"The Chilean ambassador to Israel was summoned to the Director General of the Ministry of Foreign Affairs on Sunday for a reprimanding conversation in which the Israeli response will be clarified to the ambassador."

President Boric is known as a strident critic of Israel. He has previously called Israel a "murderous" country, and supported a boycott of products from the settlements. In 2019, the Jewish community in Chile sent Boric a jar of honey in honour of Rosh Hashanah. He then wrote on Twitter: "I appreciate the gesture but they could start by asking Israel to return the illegally occupied Palestinian territory."

Chile’s Jewish community slammed the refusal as a “serious diplomatic incident", while the American Jewish Committee labelled the move “unprecedented” and said Boric must apologize or risk irreparable harm to Israel-Chile ties, his connection to the Chilean Jewish community, as well as Chile’s international reputation.