Israeli Prime Minister Benjamin Netanyahu has said his country "deeply regrets that a stray ammunition" hit Gaza's only Catholic Church, killing three people sheltering there.

"Every innocent life lost is a tragedy. We share the grief of the families and the faithful," he said in a statement.

The incident happened on Thursday when an Israeli strike hit the Holy Family Church in Gaza City. Several people were also injured, said the Latin Patriarchate of Jerusalem which oversees the small parish.

Pope Leo XIV said he was "deeply saddened to learn of the loss of life and injury", renewing his call for a Gaza ceasefire.

In his statement, Netanyahu said Israel was "investigating the incident and remains committed to protecting civilians and holy sites".

In a statement later on Thursday, the Israel Defense Forces (IDF) said: "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 cause of the incident is under review.

"The IDF directs its strikes solely at military targets and makes every feasible effort to mitigate harm to civilians and religious structures, and regrets any unintentional damage caused to them," the statement added.

Earlier in the day, White House spokeswoman Karoline Leavitt said US President Donald Trump did not have a "positive reaction" to the attack on the church.

Trump called Netanyahu to discuss the incident on Thursday morning. During the call, Netanyahu described the attack as a "mistake", Leavitt cited him as saying.

The Patriarchate said the parish priest, Father Gabriel Romanelli, was a part of those who had been injured in the attack.

It said that people found a "sanctuary" in the church "hoping that the horrors of war might at least spare their lives after their homes, possessions, and dignity had already been stripped away".

It added that the "war must come to a complete end".