Prime Minister Benjamin Netanyahu expressed regret after Israeli tank fire killed three people at a Catholic church in Gaza on Thursday, blaming a "stray" round for the deaths after a phone call with US President Donald Trump.

The Latin Patriarchate of Jerusalem said 10 others were also wounded in the attack on the Holy Family Church in Gaza City — the territory's only Catholic house of worship — including parish priest Father Gabriel Romanelli.

Witnesses and the Latin Patriarch said a tank shell slammed directly into the church around 10:30 AM (0730 GMT), but the Israeli military later said an initial inquiry "suggests that fragments from a shell... hit the church mistakenly."

Pope Leo XIV said he was "deeply saddened" by the loss of life at Holy Family, which the late Pope Francis had kept in regular contact with throughout the war between Israel and Hamas militants.

Israel's military maintained it made "every feasible effort to mitigate harm to civilians and religious structures", while Netanyahu promised an investigation.

"Israel deeply regrets that a stray ammunition hit Gaza's Holy Family Church. Every innocent life lost is a tragedy," Netanyahu said in a statement.

White House Press Secretary Karoline Leavitt said Trump had called Netanyahu after having "not a positive reaction" to news of the strike.

"It was a mistake by the Israelis to hit that Catholic church, that's what the prime minister relayed to the president," she said.

AFP images showed the injured being treated at Gaza City's Al-Ahli Hospital, also known as the Baptist Hospital, with one receiving oxygen and blood while lying under a foil blanket. Father Romanelli could be seen with a bandage around his lower leg.

Mourners knelt next to two white body bags laid out on the floor.

"In the morning a tank shell targeted us and hit the church, and a number of civilians were killed and wounded," said Shadi Abu Daoud, a displaced man whose 70-year-old mother was killed in the strike.

Gaza civil defence spokesman Mahmud Bassal confirmed the deaths at the church.

Cardinal Pierbattista Pizzaballa, the Latin Patriarch of Jerusalem, told Vatican News: "What we know for sure is that a tank, the IDF (Israeli military) says by mistake, but we are not sure about this, they hit the Church directly."

'Serious act'

The patriarchate, which has jurisdiction for Catholics in Israel, the Palestinian Territories, Jordan and Cyprus, said it "strongly condemns this strike and this targeting of innocent civilians".

The site was sheltering around 600 displaced people, the majority of them children and 54 with special needs.

"The people in the Holy Family Compound are people who found in the Church a sanctuary -- hoping that the horrors of war might at least spare their lives, after their homes, possessions and dignity had already been stripped away," it said in a statement.

Foreign leaders, including from France and Italy, called the attack "unacceptable."

Gaza's civil defense agency reported that Israeli strikes elsewhere across the Palestinian territory killed at least 22 people on Thursday.

Out of the Gaza Strip's population of more than two million, about 1,000 are Christians. Most of them are Orthodox but according to the Latin Patriarchate, there are about 135 Catholics in the territory.

Pope Francis had repeatedly called for an end to the Gaza war, condemning in his final Easter message a day before his death the "deplorable humanitarian situation" in the Palestinian territory.

'Totally unacceptable'

Monsignor Pascal Gollnisch, the head of Catholic charity l'Oeuvre d'Orient, told AFP the raid was "totally unacceptable."

"It is a place of worship. It is a Catholic church known for its peaceful attitude, for being a peacemaker. These are people who are at the service of the population," he said.

"There was no strategic objective, there were no jihadists in this church. There were families, there were civilians."

More than 21 months of war have created dire humanitarian conditions for Gaza's population, displacing most residents at least once and triggering severe shortages of food and other essentials.

The war was triggered by the October 7, 2023 Hamas attack on Israel, which resulted in the deaths of 1,219 people, most of them civilians, according to an AFP tally based on official figures.

Israel's retaliatory military offensive has killed at least 58,667 Palestinians, mostly civilians, according to the health ministry in Hamas-run Gaza.

Media restrictions in Gaza and difficulties in accessing many areas mean AFP is unable to independently verify the tolls and details provided by the civil defense agency and other parties.