Abbas condemned anti-Semitism and called the Holocaust the "most heinous crime in history" in a statement issued by his office in Ramallah after a four-day meeting of the Palestinian National Council (PNC).
"If people were offended by my statement in front of the PNC, especially people of the Jewish faith, I apologize to them. I would like to assure everyone that it was not my intention to do so, and to reiterate my full respect for the Jewish faith, as well as other monotheistic faiths," the statement said.
"Likewise, we condemn anti-Semitism in all its forms, and confirm our commitment to the two-state solution, and to live side by side in peace and security," he said.
Israeli Defense Minister Avigdor Lieberman however, rejected Abbas’s apology, labelling him a wretched Holocaust denier.”
In his speech Monday, the Palestinian leader repeated conspiracy theories about the Jews' origins and their ties to the land of Israel.
"The Jewish question that was widespread throughout Europe was not against their religion, but against their social function, which relates to usury and banking and such," Abbas said.
He claimed Nazi leader Adolf Hitler offered the Jews money incentives to emigrate out of Europe to Palestine, including the option of taking all of their assets with them and selling their real state in the continent.
"He (Hitler) wanted the Jewish homeland (in Palestine) to be supportive of him," the Palestinian leader said.
Abbas also spoke about the roots of European Jewry, quoting a historian called Arthur Koestler who wrote about a "13th tribe" of Israel in the "Khazar Kingdom"—a theory that has been dismissed by other Jewish historians.
The Khazar Kingdom, Abbas said, eventually collapsed and its subjects spread throughout Europe. Those subjects, Abbas asserted, are the Ashkenazi Jews.
"They have no relationship to Semitic culture, Abraham, Jacob and others," Abbas claimed.
He also compared the treatment of European Jews to that of Jews who lived in Arab nations, saying the latter never suffered from persecution in the 1,400 years they lived there.
UN Middle East envoy Nickolay Mladenov called Abbas' comments "deeply disturbing".
President Reuven Rivlin questioned Wednesday how Abbas could be considered a legitimate peace partner in light of his speech.
“How can a leader who expresses such dark anti-Semitic ideas present himself as a partner in peace?” Rivlin asked during a state visit to Ethiopia.
The European Union's foreign service also condemned Abbas’s "unacceptable” remarks, echoing criticism on Wednesday by Prime Minister Benjamin Netanyahu. US officials also condemned on Tuesday night Abbas's speech.
A veteran member of Fatah, the PLO's dominant faction, Abbas served for decades as a loyal deputy of his predecessor, Yasser Arafat. He assumed the leadership of Fatah, the PLO and the Palestinian Authority after Arafat died in 2004, and was re-elected as chairman of the PLO's Executive Committee on Friday.
This is not the first time he has been accused of anti-Semitism. In 1982 Abbas obtained a doctorate in history at the Moscow Institute of Orientalism in the then-Soviet Union. His dissertation, entitled "The Secret Relationship between Nazism and the Zionist Movement", drew widespread criticism from Jewish groups.
The following year the Simon Wiesenthal Center released translated quotations from the book, including one excerpt about World War Two in which, according to the center's translation, Abbas wrote:
"Following the war...word was spread that six million Jews were amongst the victims and that a war of extermination was aimed primarily at the Jews...The truth is that no one can either confirm or deny this figure. In other words, it is possible that the number of Jewish victims reached six million, but at the same time it is possible that the figure is much smaller—below one million."
After Abbas' speech on Monday, Hier and Cooper said: "The world can now see that see that, for Palestinian Authority President Abbas, nothing has changed in the 45 years since his doctoral dissertation was first published."
Itamar Eichner, Shahar Hay and Reuters contributed to this report.