Israel provided no immediate explanation for not being present at the session dedicated overwhelmingly to discussion of its policies and alleged abuses, but a source close to the council said its absence clearly amounted to a boycott.
"We won't comment on that," a spokeswoman with the Israeli mission in Geneva told AFP.
The United States was also absent from today's discussions.
Asked for an explanation, a spokesman said only that the US ambassador to the council Keith Harper was in Washington.
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"The process cannot be rushed," former New York judge Mary McGowan Davis, who has taken over as head of the team, told the council.
Canadian international law expert William Schabas resigned as chair of the Commission of Inquiry on the 2014 Gaza conflict last month after Israel complained he could not be impartial because he had prepared a legal opinion for the Palestine Liberation Organisation in October 2012.
Israel was not satisfied, calling for the entire inquiry to be shelved, insisting the commission and the Human Rights Council which created it are inherently biased against the Jewish state.
The Jewish state is the only country in the world with a special agenda item dedicated to it, meaning its rights record is discussed at every session of the UN's top rights body.
It cut all ties with the council in March 2012 over its plans to probe how Jewish settlements were harming Palestinian rights, and did not resume relations until late 2013.
Today's session came after Prime Minister Benjamin Netanyahu's right-wing Likud party scored an unexpected election victory last week.