"It would be appropriate also to say at this time to Mr. Obama that you are now a civilian and I am sorry for uttering those words," Duterte said during a speech given in Jerusalem on Sunday.
The Philippine president said he has forgiven Obama for criticizing his crackdown on illegal drugs. Several world leaders and the United Nations have accused Duterte of human rights violations.
Duterte is in Israel for a four-day visit. He is expected to agree to a deal to purchase Israeli oil and arms.
The controversial Philippine president made headlines when he compared his war on drugs to the Holocaust and likened himself to Hitler. But Sunday, while visiting a Holocaust memorial in Israel, Duterte vowed to fight "insane rulers" like Hitler.
Duterte said the Philippines and Israel "share the same passion for peace."
"Israel can expect any help that the Philippines can extend," he said at the ad Vashem Holocaust memorial.
In the memorial's guest book, Duterte reportedly wrote: "Never again. May the world learn the lessons of this horrific and benighted period of human history."
In the same speech that Duterte apologized to Obama, he called the former United State president "cold" and "always at a distance." In contrast, the Philippine president said President Donald Trump is a "good friend."
Duterte has previously said he and President Trump speak "the same language."
The Philippine president has faced condemnation for urging Filipinos not to wear condoms and joking about rape.