But the reversal, which could face a legal battle, likely won't apply to the more than 2,300 children who have already been separated from their parents, the Department of Health and Human Services said.
"There will not be a grandfathering of existing cases," Kenneth Wolfe, a spokesman for the department's Administration for Children and Families, told The New York Times on Wednesday. Wolfe acknowledged that the White House would ultimately decide on the children's fate, but noted: "I can tell you definitively that is going to be policy."
The departments of Homeland Security and Health and Human Services did not immediately respond to HuffPost's requests for clarification on Wednesday.
The children who have already been separated from their parents by Border Patrol agents reportedly range from infants to teens.
"They're in crisis. They're just crying uncontrollably," one immigrant rights activist told the Times. "We've seen young kids having panic attacks, they can't sleep, they're wetting the bed. They regress developmentally, where they may have been verbal but now they can no longer talk."
Trump's executive order states the administration will "maintain family unity, including by detaining alien families together where appropriate and consistent with law and available resources. It is unfortunate that Congress's failure to act and court orders have put the Administration in the position of separating alien families to effectively enforce the law."
The order follows an outcry from Republican and Democratic lawmakers, human rights advocates, religious leaders and others over stories and images of migrant children being taken from their parents and detained, sometimes in metal cages.
Trump and other administration officials, including Department of Homeland Security Secretary Kirstjen Nielsen, defended the policy up to the last minute, insisting that they enacted it in part because of a 2015 court order that cited a 1997 settlement known as the Flores agreement that says children cannot be held in long-term detention, even with their parents.
By reversing the family separation policy but continuing to aggressively prosecute adult undocumented immigrants ― while detaining their children alongside them ― the Trump administration could be setting itself up for a legal battle with human rights activists over the Flores agreement.