The 73-year-old said on Sunday he would seek to re-affirm and renew relations with the two countries, where an estimated 76,000 Filipinos live and work.
“I leave today for landmark visits that underscore our vision for our country – a responsible member of the world community – a Philippines that is friend to all and an enemy to no one,” Duterte said before departing for Tel Aviv.
Duterte is eager to improve security cooperation with Israel, which has sold the Philippines three radar systems and 100 armoured vehicles, and which Manila is now eyeing for an aircraft deal.
According to Israeli government data, exports to the Philippines were worth $143m in 2017.
“[The visit] is for President Duterte to look for an alternative market for … weapons for our armed forces, as well as for the police,” Henelito Sevilla, an international relations expert at the University of the Philippines, told the AFP news agency.
Duterte will also visit the Yad Vashem Holocaust memorial in Jerusalem and the Open Doors Monument, a memorial to Filipinos who saved Jews from Nazi persecution.
“Hitler massacred three million Jews. Now, there are three million drug addicts [in the Philippines]. I’d be happy to slaughter them,” he said in 2017. Most mainstream historians say six million Jews died in the Holocaust.
Duterte, who took office in 2016, later apologised for his remarks, which he said were aimed at critics who had likened him to the Nazi leader.
Late last year, the Philippines abstained from a vote at the United Nations General Assembly rebuking the US for moving its embassy to from Tel Aviv to Jerusalem, a controversial decision that sparked widespread international condemnation and large-scale protests.
Palestinian leaders see occupied East Jerusalem as the capital of their future state.
Duterte on Sunday expressed support for a two-state solution to the Israeli-Palestinian conflict.
“We shall be guided by our constitution and laws as well as our international commitments in support of efforts and initiatives including the two-state solution,” he told reporters.
Israel’s foreign ministry said in a statement that it “assign(s) great importance to this visit, which symbolises the strong, warm ties between our peoples as well as the enormous potential for developing and strengthening the relations”.
Duterte will be in Israel until Wednesday, before going to Jordan until September 8. In Amman, he is expected to meet King Abdullah II.