She said information received from US civil society groups indicated that several hundred children had been separated from their parents at the border since October, including a one-year-old.
"The US should immediately halt this practice," she told reporters in Geneva.
"The practice of separating families amounts to arbitrary and unlawful interference in family life, and is a serious violation of the rights of the child."
"The use of immigration detention and family separation as a deterrent runs counter to human rights standards and principles," she said.
Bad legislation to blame: Trump
In a tweet, President Trump said "separating families at the Border is the fault of bad legislation passed by the Democrats".
"Border security laws should be changed but the Dem(ocrat)s cant get their act together. Started the Wall," he added, referring to the building of a fence meant to halt illegal crossings into the US which he made a key campaign pledge.
Separately, US Attorney General Jeff Sessions told a conservative US radio show that separating children from their parents was legal and necessary.
"You can't be giving immunity to people who bring children with them recklessly and improperly and illegally. They should never do that," he told the Hugh Hewitt Show.
Sessions announced early last month that there would be a zero tolerance policy, with all those without papers crossing into the US charged with illegal entry before they could submit a request for political asylum.
Children's interests first
Shamdasani stressed that children's rights were "generally held in high regard" in the United States, but she lamented that the country was the only one in the world that had not yet ratified the UN Convention on the Rights of the Child.
Despite this, she insisted that Washington was bound by international human rights laws that its current practices were flouting.
"The child's best interest should always come first, including over migration management objectives or other administrative concerns," she said.
"It is therefore of great concern that in the US, migration control appears to have been prioritised over the effective care and protection of migrant children."
"Detention is never in the best interests of the child and always constitutes a child rights violation," she said, calling on Washington to "adopt non-custodial alternatives that allow children to remain with their families."
The US says the policy aims to stem a surge of poor families mostly from Guatemala, El Salvador and Honduras pouring into the United States.
Citing the daily violence in their home countries, thousands each week cross the US-Mexico border and immediately turn themselves in to authorities asking for asylum.
William Spindler of the UN refugee agency stressed Tuesday that "the right to claim asylum is a fundamental human right... and it is also part of the law in the United States."