GENEVA — The Trump administration’s practice of separating children from migrant families entering the United States violates their rights and international law, the United Nations human rights office said on Tuesday, urging an immediate halt to the practice.

The administration angrily rejected what it called an ignorant attack by the United Nations human rights office and accused the global organization of hypocrisy.

The human rights office said it appeared that, as The New York Times revealed in April, United States authorities had separated several hundred children, including toddlers, from their parents or others claiming to be their family members, under a policy of criminally prosecuting undocumented people crossing the border.

That practice “amounts to arbitrary and unlawful interference in family life, and is a serious violation of the rights of the child,” Ravina Shamdasani, a spokeswoman for the Office of the United Nations High Commissioner for Human Rights, based in Geneva, told reporters.

Last month, the Trump administration announced a “zero tolerance” policy for illegal border crossings, saying that it would significantly increase criminal prosecutions of migrants. Officials acknowledged that putting more adults in jail would mean separating more children from their families.

“The U.S. should immediately halt this practice of separating families and stop criminalizing what should at most be an administrative offense — that of irregular entry or stay in the U.S.,” Ms. Shamdasani said.

The United States ambassador to the United Nations, Nikki R. Haley, clearly showed American irritation with the accusation in a statement released a few hours later.

“Once again, the United Nations shows its hypocrisy by calling out the United States while it ignores the reprehensible human rights records of several members of its own Human Rights Council,” Ms. Haley said. “While the High Commissioner’s office ignorantly attacks the United States with words, the United States leads the world with its actions, like providing more humanitarian assistance to global conflicts than any other nation.”

Without addressing the specifics of the accusation, Ms. Haley said: “Neither the United Nations nor anyone else will dictate how the United States upholds its borders.”

The administration has characterized its policy as being about illegal immigration, though many of the detained migrants — including those in families that are split apart — enter at official border crossings and request asylum, which is not an illegal entry. It has also said that some adults falsely claim to be the parents of accompanying children, a genuine problem, and that it has to sort out their claims.

On Twitter, President Trump has appeared to agree that breaking up families was wrong, but blamed Democrats for the approach, saying that their “bad legislation” had caused it. In fact, no law requires separating children from families, and the practice was put in place by his administration just months ago.

The Times found in April that over six months, about 700 children had been taken from people claiming to be their parents.

The American Civil Liberties Union says that since then, the pace of separations has accelerated sharply. Lee Gelernt, deputy director of the group’s immigrant rights project, said that in the past five weeks, close to 1,000 children may have been taken from their families.

Last year, as Homeland Security secretary, John F. Kelly raised the idea of separating children from their families when they entered the country as a way to deter movement across the Mexican border.

Homeland Security officials have since denied that they separate families, but have also faced sharp criticism from Mr. Trump for failing to do more to curb the numbers of migrants crossing the border.

For the United Nations, it was a matter of great concern that in the United States “migration control appears to have been prioritized over the effective care and protection of migrant children,” Ms. Shamdasani said.

The United States is the only country in the world that has not ratified the Convention on the Rights of the Child, she noted, but the practice of separating and detaining children breached its obligations under other international human rights conventions it has joined.

“Children should never be detained for reasons related to their own or their parents’ migration status. Detention is never in the best interests of the child and always constitutes a child rights violation,” she said, calling on the authorities to adopt noncustodial alternatives.

The A.C.L.U. has filed a class-action lawsuit in federal court in San Diego, calling for a halt to the practice and for reunification of families.