White House spokeswoman Caroline Levitt told reporters that Trump had called Netanyahu after the US president's "unfavorable reaction" to learning of the strike.
"The Israelis' targeting of the Catholic Church was a mistake, that's what the prime minister told the president," she added.
Earlier Thursday, Israel bombed the Holy Family Church east of Gaza City, killing three people and wounding nine, including one in critical condition and two in serious condition. The parish priest, Father Gabriele Romanelli, and the Latin Patriarchate in Jerusalem sustained minor injuries.
The Church of the Holy Family is one of the oldest Christian religious centers in the Gaza Strip. Since the beginning of the Israeli genocide, it has become a haven for civilians, particularly Christian families facing displacement and siege.
During the Israeli genocide in Gaza, the Israeli occupation army bombed three major churches: the Church of St. Porphyrius, the Church of the Holy Family, and the Baptist Church, in addition to dozens of hospitals, mosques, and schools.
Since October 7, 2023, Israel, with American support, has been committing genocide in Gaza, leaving more than 198,000 Palestinians dead or wounded, most of them children and women, and more than 10,000 missing. Hundreds of thousands have been displaced, and famine has claimed the lives of many, including children, as well as widespread destruction.