Israel's Foreign Ministry released a brief message on X a few hours after the news of Pope Francis' passing, "Rest in peace, Pope Francis. May his memory be a blessing." Several hours later, it was deleted without explanation.

The decision to delete the post came at a time when people around the world were mourning Pope Francis' death. It seemed to reflect the growing tensions between Israel and the Vatican, due to the pope's frequent criticism of Israel's actions during the Gaza war. The Israeli Foreign Ministry refused to comment on the deletion. Normally, Prime Minister Benjamin Netanyahu is quick to release statements when major international figures pass away, but he has remained silent about the pope's death. The same goes for Foreign Minister Gideon Saar. The only official condolences came from Israel's president, Isaac Herzog, who holds a mostly ceremonial role. He praised Pope Francis for his deep faith and immense compassion. During most of Pope Francis' papacy, the relationship between Israel and the Vatican improved, highlighted by his visit to the Holy Land in 2014. However, everything changed after the war in Gaza broke out following Hamas' deadly attack in southern Israel on October 7, 2023.

While Pope Francis expressed sympathy for the Israeli victims and hostages, he also suggested that Israel's attacks on Gaza and Lebanon afterwards were immoral and excessive. He called for an investigation to determine if Israel's actions in Gaza could be considered genocide, a claim Israel denies as investigations at the UN's top courts continue. Pope Francis condemned the events of October 7, but he also made it clear that what happened on that day did not justify the ongoing violence since then, according to Wadie Abunassar, who represents Christians in Israel and the Palestinian territories. Abunassar described Pope Francis as a friend who tells the truth, even when it's not what you want to hear.

During the war, Pope Francis managed a difficult balance between his strong ties with Israel and speaking out against the devastating losses in Gaza, according to Amnon Ramon, an expert on Christianity in Israel and senior researcher at the Jerusalem Institute for Policy Research. Francis had a close relationship with the local parish priest in Gaza, who, like the pope, is from Argentina.

Israel and the Vatican have had a strained relationship for a long time. This tension dates back to World War II, when critics claim Pope Pius XII stayed silent about the Holocaust, despite possibly knowing about the Nazi plan to kill the Jews. Supporters argue that he used quiet diplomacy to save Jewish lives. In the 1960s, the Vatican went through major changes, including a shift in how the Church viewed Jews, particularly regarding the belief that Jews were collectively responsible for Jesus' crucifixion, as Ramon explained.

In 1993, the Holy See officially began diplomatic relations with Israel. Christians make up less than 2% of the population in Israel, with around 182,000 in Israel, 50,000 in the West Bank, and 1,300 in Gaza, according to the US State Department. When Pope Francis became pope, the relationship between the Vatican and Israel improved a lot. One of his first international trips in 2014 was to the Holy Land, where he met with then-Israeli Prime Minister Netanyahu. Former President Shimon Peres also visited the Vatican several times, including when he and Palestinian Authority President Mahmoud Abbas planted a peace tree in the Vatican Gardens.

The Israeli government's shift to the right, along with the ongoing war with Gaza, has caused tensions. Pope Francis expressed his concern about hostages held in Gaza. He spoke out for the first time on October 8, the day after the war began, and continued to emphasise throughout his life that war is a defeat, and there is no real victory in war, according to Rev. David Neuhaus, a local priest and spokesperson during the pope's visit in 2014. The pope showed deep concern for the hostages but also stated that violence should stop, as Israel is using force to achieve something that cannot be solved by force, Neuhaus added.

Pope Francis also met with the families of hostages held in Gaza, as well as Palestinians affected by the conflict. In an interview with The Associated Press in April 2023, Cardinal Pierbattista Pizzaballa, the leader of Catholics in the Holy Land, mentioned that Netanyahu's far-right government has made life harder for Christians in the place where Christianity began. He pointed out the rise in attacks on Christian sites, pilgrims, and religious leaders. 

Although world leaders like US President Donald Trump and French President Emmanuel Macron are expected to attend the pope's funeral, Israel will only send its ambassador to the Vatican, a lower-level diplomat. Oren Marmorstein, a spokesperson for Israel’s Foreign Ministry, explained that this decision is partly due to scheduling conflicts and the funeral falling on Saturday, the Jewish Sabbath, which means Israeli politicians need to remain close to the funeral. He stressed that this was not meant to signal any tension between Israel and the Vatican. Israel will be represented at the funeral by our ambassador there, said Marmorstein. Although we didn’t agree on everything, we are still participating in the funeral.

Pope Francis focused on the theme of mercy in today’s divided world. Abunassar, the coordinator of the Holy Land Christian Forum, stated that while Pope Francis was a great friend of Israel, the Israeli leadership failed to understand him properly. Abunassar, a Catholic from Haifa, expressed frustration that the Israeli government had only sent condolences through the president and not in an official capacity. He said, "The pope was the leader of the world’s most important church, the head of state, and had followers who are Israeli taxpayers. He deserved more respect."

Prime Minister Netanyahu had publicly expressed condolences for the passing of other world leaders, including Queen Elizabeth II and former President Jimmy Carter, who was critical of Israel. On Wednesday, hundreds gathered at the Church of the Holy Sepulchre, where tradition says Jesus was crucified, buried, and resurrected, for a special requiem mass in honour of Pope Francis. Representatives from Orthodox Christianity were also present, reflecting Francis' strong support for interfaith relations, especially following his landmark meeting with Ecumenical Patriarch Bartholomew I of Constantinople in 2014, which helped ease tensions between their churches after centuries of conflict. Neuhaus expressed hope that the next pope would continue Francis' message, saying, "I hope it will be someone who emphasises mercy and can bring us all together. We live in such a divided, polarised world."