Over 2,290 refugee and asylum seeker children were held in Thailand, Malaysia and Indonesia at the end of 2016, according to Save the Children and the Asia Pacific Refugee Rights Network in a report released on Thursday.
The three nations have been on key transit routes for thousands of migrants and asylum seekers, from countries including Myanmar, Bangladesh and Afghanistan, who are trying to flee violence or poverty at home to reach Australia.
But they are often intercepted during these journeys, and authorities typically treat asylum seekers and refugees as illegal immigrants, subjecting them to arrest or detention.
"These children should not be treated like criminals," said Mike Novell, Save the Children's interim director for Asia.
"The impact this environment has on children is extremely damaging... It can lead to developmental delays and self-harm while putting children at very real risk of violence, sexual abuse and exploitation."
Based on analysis of immigration policies and interviews with a small number of child detainees, the report found children often being detained with unrelated adults and separated from their families.
Some were forced to sleep in "cramped and substandard" conditions, including on cardboard or directly on the floor, the report said, and were given food that was "unpalatable".
It found some children were housed in cells so hot it was difficult to breathe, and on some occasions in rooms so overcrowded they could not lie down at night with their legs fully extended.
"There's a lot of germs... the weather was so hot... we cannot breathe ourselves easily because it's really hot inside," the report quoted a 14-year-old girl, who was detained in a cell with 150 other people, as saying.
The charities said although the number of child detainees in Asia-Pacific had fallen by over 50 percent at the end of 2016 compared with 2014, countries must move to end child detention entirely.
In Australia, where nearly all children have been released from detention in recent years, the two rights groups called for a review of the country's laws which still allow the practice.
Governments should adopt community housing or foster care for unaccompanied child instead, the charities urged, saying they are a more humane and cheaper alternative.