UN rights chief Zeid Ra'ad Al Hussein said Monday "the thought that any state would seek to deter parents by inflicting such abuse on children is unconscionable."
Human Rights Watch criticized the move, warning that Washington's absence at the top UN body would put the onus on other governments to address the world's most serious rights problems.
"The Trump administration's withdrawal is a sad reflection of its one-dimensional human rights policy: defending Israeli abuses from criticism takes precedence above all else," said HRW's executive director Kenneth Roth.
"The UN Human Rights Council has played an important role in such countries as North Korea, Syria, Myanmar and South Sudan, but all Trump seems to care about is defending Israel."
US criticism stems from the fact that Israel is the only country that has a dedicated agenda item, known as Item 7, at the rights council, meaning its treatment of the Palestinians comes under scrutiny at each of the body's three annual sessions.
The United Stated refused to join the body when it was created in 2006, when George W. Bush was in the White House and his ambassador to the UN was John Bolton, Trump's current hawkish and UN-skeptic national security advisor.