Prime Minister Benjamin Netanyahu of Israel offered condolences Thursday on the passing of Pope Francis, more than three days after the death of the Roman Catholic world’s leader.

The delay in issuing a statement highlighted apparent tensions in the relationship between Israeli officials and the pope, who pointedly criticized Israel’s conduct in the war in Gaza and repeatedly called for a cease-fire.

“The State of Israel expresses its deepest condolences to the Catholic Church and the Catholic community worldwide at the passing of Pope Francis,” the office of the Israeli prime minister said in a post on X. “May he rest in peace.”

Neither the Hebrew-language X account for the prime minister’s office nor Mr. Netanyahu’s personal account carried the short statement. Mr. Netanyahu usually issues condolence statements shortly after the deaths of world leaders.

Francis, who frequently phoned members of Gaza’s dwindling Christian community, took advantage of major addresses to the Catholic world to call for the entry of humanitarian aid to Gaza, a cease-fire and the release of hostages held by militants.

“My thoughts go especially to the victims of the many conflicts worldwide, beginning with those in Israel and Palestine,” he said during Easter Sunday Mass in 2024.

Since early March, Israel has blocked the entry of humanitarian aid into Gaza, leaving many people in Gaza struggling to access food.

In a book released in November 2024, Francis said the war in Gaza should be investigated to determine whether it constituted a genocide. The statement drew a harsh rebuke from a member of Mr. Netanyahu’s government, Amichai Chikli, the minister of diaspora affairs, who contended it was a “trivialization” of the term genocide. Israeli officials say that Israel is waging a war against Hamas in Gaza and not civilians. They also argue that it is Hamas that should face charges of genocide after its attack on Oct. 7, 2023, when about 1,200 people were killed in Israel and roughly 250 were taken captive. The pope also met with the families of Israelis taken hostage by Hamas.

More than 51,000 people in Gaza have been killed since the war began, according to the health ministry in the territory, which does not distinguish between civilians and combatants.

In 2014, Francis visited Israel and the Israeli-occupied West Bank, where he called for a “sovereign homeland” for Palestinians. He also became the first pontiff to refer to the occupied territory as “the State of Palestine.”

Isaac Herzog, Israel’s largely ceremonial president, was one of the first leaders to issue a statement mourning the death of Francis.

But on the day of the pope’s death, Israel’s Foreign Ministry issued a statement on X, saying ”may his memory be a blessing.” But shortly thereafter, the ministry deleted the post.

After facing criticism in Israel, the ministry reposted a picture of its ambassador to the Holy See, Yaron Sideman, visiting the pope’s coffin in the Vatican. Ambassador Sideman will represent Israel at the pope’s funeral, according to Oren Marmorstein, the Foreign Ministry spokesman.

In a statement, Mr. Marmorstein did not explicitly address the deletion of the X post, but emphasized that Israeli diplomats around the world have offered their condolences on social media and signed official condolence books.

Aaron Boxerman contributed reporting.