The removal of the Israeli Foreign Ministry's condolences is seen as another sign of the strained relationship between Israel and the Vatican.
Prime Minister Benjamin Netanyahu, who often quickly issues statements when important international figures pass away, delivered his condolences for the first time on Thursday, three days after the death announcement.
"The State of Israel expresses its deepest condolences to the Catholic Church and the Catholic community worldwide on the passing of Pope Francis. May he rest in peace," writes Netanyahu's office on X.
Israel's President Isaac Herzog sent his condolences on Monday and wrote that the Pope was "a man of deep faith and boundless compassion".
The ties between Israel and the Vatican strengthened during Pope Francis' first year, but deteriorated after the war in Gaza broke out following the terrorist-stamped Hamas attack on Israel on October 7, 2023.
The Pope has, among other things, said that it should be investigated whether Israel's attacks on Gaza amount to genocide. He also expressed concern for the hostages held by Hamas in Gaza.