President George W Bush had stopped paying UN fees but under his presidency, the US had not left the UN.
"But we are living in strange time with a president who is withdrawing from one international organisation and agreement after another," Clark said, referring to the Paris agreement on climate change, the Trans Pacific Partnership and the Iran nuclear deal.
US ambassador to the UN Nikki Haley said the Human Rights Council was a "cesspool of political bias" and a "protector of human rights abusers".
While the US has threatened the withdrawal of the council for several months, it was confirmed a day after the UN High Commissioner for Human Rights condemned the separation of children from undocumented parents at the border with Mexico as "unconscionable".
The Human Rights Council is a UN organisation comprising 47 members and is based in Geneva.
Helen Clark said no one was lily white. The US on the council had rightly raised issues about authoritarian regimes but "it also needs to be conscious of the rights of small children being ripped away from their parents".
"It's very hard to say someone's on the side of the angels here and someone isn't."
Foreign Minister Winston Peters said today the withdrawal of the US from the Human Rights Council was very concerning because it had been a great contributor in the past.
He did not know yet what the implications would be, besides the funding cut which would be serious in itself.
Peters himself was a little more critical of what is happening on the US border than he was on Tuesday when he said he wanted to focus on New Zealand. Not other countries.
The Greens put out a statement on Wednesday calling on him to criticise the United States.
Talking to reporters a short time later, Peters said: "There is not a cabinet minister or Member of Parliament that is not concerned about that."
Asked if would write to US ambassador Scott Brown or call him in, Peters said "We are not going to have a contest to see who is most outraged."
It was an internal debate within the US and New Zealand was watching with interest.
Asked if it was inhumane, he said "it is a whole lot of things and that is a description you could use as well".
"We do not think that is the way to treat people and we do not do that in our country."
New Zealand raised such issues with other countries in the right forums whether it was with Japan over whaling or with China over Tibet.
"To be putting out masses of press statements as though you are the only one that cares is somewhat superficial... if you want a contest of whose can be most suitably outraged, then I'm not going to win it."
Clark was speaking from Canada where she received two honorary doctorates.
Canada has just voted to legalise the use of recreational cannabis, which Clark supports.
