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

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

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 Prime Minister’s Office added in a statement.

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

“He called Prime Minister Netanyahu this morning to address the strikes on that church in Gaza,” Leavitt said.

She continued, “The prime minister agreed to put out a statement that it was a mistake by the Israelis to hit that Catholic Church. That’s what the prime minister relayed to the president.”

In a Vatican telegram on Thursday, a church official said Pope Leo XIV is “deeply saddened” following the strike.

Calling the strike a “military attack,” the Vatican’s Secretary of State Pietro Parolin said: “In commending the souls of the deceased to the loving mercy of Almighty God, the Holy Father prays for the consolation of those who grieve and for the recovery of the injured.”

Netanyahu’s office also said they are “grateful to Pope Leo for his words of comfort.”

The Latin Patriarchate of Jerusalem, which has jurisdiction for Latin-rite 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 ongoing war.

The Israel Defense Forces (IDF) has 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,” the statement added.

The IDF said earlier on Thursday that it was “aware of reports regarding damage caused to the Holy Family Church in Gaza City and casualties at the scene,” adding that “the circumstances of the incident are under review.”

“The (Israel Defense Forces) makes every feasible effort to mitigate harm to civilians and civilian structures, including religious sites, and regrets any damage caused to them,” it said.

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

“We pray for the rest of their souls and for the end of this barbaric war. Nothing can justify the targeting of innocent civilians,” its statement read.

Pope Leo used his statement to reiterate his plea for an immediate ceasefire in Gaza.

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.

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 Latin Patriarchate of Jerusalem.

The church is known internationally for its close connection with the late Pope Francis, who would call the parish almost daily since the beginning of the Israel-Hamas war.

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 Gaza ceasefire 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 positioning of Israeli troops in Gaza around the Morag Corridor during a proposed 60-day ceasefire has been a major stumbling block in the talks.

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 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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