By Ibrahim Dahman, Catherine Nicholls, Christopher Lamb, Abeer Salman, Eugenia Yosef and Sophie Tanno, CNN

(CNN) — Israel said Thursday that it “deeply regrets” a deadly strike on Gaza’s only Catholic church, which killed three people.

The Latin Patriarchate of Jerusalem, which has jurisdiction for Roman Catholics in Gaza, said the Holy Family Church was struck by Israel on Thursday morning. The church has become a shelter for the enclave’s tiny Christian community amid the 20-month war.

The office of Israel’s Prime Minister Benjamin Netanyahu said that “Israel deeply regrets that a stray ammunition hit Gaza’s Holy Family Church. Every innocent life lost is a tragedy.”

“Israel is investigating the incident and remains committed to protecting civilians and holy sites,” the office added in a statement.

Pope Leo received a phone call from Netanyahu on Friday, following the strike, the Vatican said, in which the patriarch expressed the importance of protecting places of worship.

During the phone call, which Netanyahu’s office is yet to comment on, Leo renewed his calls for a ceasefire to be reached by the warring sides in Gaza, a statement said.

Pope Leo “again expressed his concern for the dramatic humanitarian situation of the population in Gaza, whose heartbreaking price is paid especially by children, the elderly and the sick,” according to the statement.

Leaders from the Catholic and Greek Orthodox Church visited the church on Thursday, in a highly unusual trip given Israel’s tight control over access in and out of the territory.

Cardinal Pierbattista Pizzaballa, the Latin Patriarch of Jerusalem, together with Theophilos III, the Greek Orthodox Patriarch of Jerusalem, visited the enclave to show their support for Gaza’s Catholics, according to a statement from the Latin Patriarchate of Jerusalem.

The two expressed “the shared pastoral solicitude of the Churches of the Holy Land and their concern for the community of Gaza,” according to a statement from the Jerusalem Patriarchate.

Netanyahu told US President Donald Trump in a phone call that the church incident was a “mistake,” White House press secretary Karoline Leavitt told a briefing Thursday. Asked about Trump’s view on the strike, Leavitt described it as “not a positive reaction.”

The Israel Defense Forces acknowledged it hit the church “mistakenly.”

“An initial inquiry into reports regarding injured individuals in the Holy Family Church in Gaza City, suggests that fragments from a shell fired during operational activity in the area hit the church mistakenly,” the IDF said in a statement on Thursday.

“The cause of the incident is under review.”

Church ‘directly’ hit

Cardinal Pierbattista Pizzaballa, the Latin Patriarch of Jerusalem, told Vatican News that the church was hit “directly” by a tank Thursday morning.

The parish priest, Father Gabriel Romanelli, was injured in the attack, the patriarchate said, alongside a number of others. Romanelli is an Argentine who has ministered in Gaza for close to 30 years.

It named the three killed as Saad Issa Kostandi Salameh, Foumia Issa Latif Ayyad and Najwa Abu Dawood. Several others were also injured.

Images verified by CNN showed the church was damaged in the attack, but the crucifix on top of the church’s roof appeared intact.

The church has come under attack once before amid Israel’s war in Gaza. In December 2023, an Israeli military sniper shot and killed two women who were sheltering inside, according to the patriarchate.

The church is known internationally for its close connection with the late Pope Francis, who would call the parish almost daily as the war raged on.

Only around 1,000 Christians are thought to have lived in Gaza before the October 7 attacks, which is overwhelmingly a Muslim territory.

Meanwhile ceasefire talks to end the war in Gaza, which Palestinian officials say has killed over 58,000 people, are continuing.

Israel may show flexibility on a key sticking point in the talks, sources have told CNN, as negotiators attempt to close the gaps preventing the first pause in months of fighting.

Specifically, there could be some flexibility from Israel on the potential withdrawal of its troops from the Morag Corridor – a key Israeli security zone in the southern Gaza strip – a source familiar with the matter told CNN on Thursday.

The corridor was established by Israeli forces in April with the stated intention of dividing up Gaza and exerting greater pressure on Hamas. Its name refers to the Jewish settlement of Morag that once lay between the cities of Khan Younis and Rafah in the south of the territory.

The US had talked up the prospects of a quick agreement in the talks, which had gained momentum after a deal ended the brief Israel-Iran conflict last month. But days of talks yielded no breakthrough.

This story has been updated with additional developments.

CNN’s Mohammed Tawfeeq contributed to this report.

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