LOS ANGELES — The Trump administration intentionally separated thousands of migrant children from their parents at the southern border in the spring of 2018, an aggressive attempt to discourage family crossings that caused lasting trauma and drew widespread condemnation.

What is only now becoming clear, however, is that a significant number of U.S. citizen children were also removed from their parents under the so-called zero tolerance policy, in which migrant parents were criminally prosecuted and jailed for crossing the border without authorization.

Hundreds, and possibly as many as 1,000, children born to immigrant parents in the United States were removed from them at the border, according to lawyers and immigrant advocates who are working with the government to find the families.

In many cases, the U.S.-born children were placed into foster care for lengthy periods, and some have yet to be reunited with their parents, lost in the system nearly five years after the separations took place.

“We don’t even know where these parents are today, and whether or not they know where their children are,” said Paige Chan, executive director of the nonprofit Together and Free, who has been working with a federal task force charged with tracking the whereabouts of separated families. “The U.S. government is only beginning to account for the number of U.S. citizens put through this unimaginable trauma.”

Some 5,500 foreign-born children were already known to have been separated from their parents under the policy. The separations usually lasted for a matter of weeks, but in some cases they lasted years.

The revelations represent the first confirmation that U.S.-born children traveling with migrant parents were also subjected to the separation policy, which became official along the entire border in April 2018 after it was piloted in El Paso the previous year.

As U.S. citizens, the children did not necessarily have any additional rights that would have prevented them from being taken from parents who were jailed, legal analysts said. In fact, it may have put them at a disadvantage: Their status as citizens automatically placed them under the oversight of state child welfare authorities, complicating efforts to keep track of them and reconnect them with parents.

While foreign-born children were transferred to shelters operated by the federal Office of Refugee Resettlement, where they were entered into federal databases and eventually allowed to speak with their parents by telephone, there was no such system for children dispatched to state foster care systems. State family courts, using varied sets of criteria, were left to decide independently how to handle the cases.

The situation became even more difficult when parents were deported.

“Theoretically, a state dependency court would determine whether it is in a child’s best interests to be reunited with a parent, even if the parent has been removed or is facing imminent removal,” said Carlos Holguin, a lawyer who has represented thousands of migrant children in federal custody.

If a judge decided against returning a child to a migrant parent and no U.S. relative was available, the child might be placed in foster care until he or she reached the age of 18, Mr. Holguin said.

Most of the children involved were born in the United States to immigrant parents who then went back to their home countries, only to return amid a worsening economy and escalating gang violence in Central America and Mexico.

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The parents of American citizens are not automatically allowed to remain in the United States, though such children after turning 21 can sponsor the undocumented parent for a green card.

Because official records are scattered and incomplete, it will take months for the government to review additional files to identify separated parents and children and then try to determine their whereabouts in the United States or abroad, said several immigrant advocates who have been working with the interagency task force, led by the Department of Homeland Security, to track the cases.

Angelo Fernandez, a spokesman for the department, confirmed that an unknown number of U.S. citizen children had been caught up in the border separations and said the task force was “combing through records” to identify them.

Leecia Welch, deputy litigation director at Children’s Rights, who litigates cases involving children at the border, said the discovery of so many U.S. citizen children added a new challenge to what had already been a vexing problem.

“When you think it can’t get any worse, you hear additional facts about the horror of the policy,” she said.

Ms. Chan said that her organization was aware of at least 226 American children who had been sent to the child protective services agency in San Diego County, Calif. Records for separated children delivered to foster care in Arizona, New Mexico and Texas do not exist, she said.

Children of a variety of ages and nationalities were caught up in the family separation policy, hundreds of whom were under 5 years old. The Trump administration said at the time that the policy was an attempt to deter the thousands of parents who officials said were putting their children in danger by taking them on perilous journeys to the border.

Removing children from parents who are being jailed is standard practice, the officials said. Children are commonly removed from U.S. citizen parents in other cases, for instance when women give birth while incarcerated, or where there has been parental abuse or neglect.

Still, images and audio of traumatized children weeping after being forcibly torn from their migrant parents caused domestic and global outrage, and the policy was rescinded.

A federal judge in California ordered the government in June 2018 to reunite separated parents and children, in response to a class-action lawsuit against the separation policy that was brought by the American Civil Liberties Union. Federal authorities facilitated reunions for parents and children who were still in custody. But many of the parents had been deported.

About 900 deported parents and siblings have since been brought back to the United States and have been allowed to remain in the country with a temporary legal status until a long-term settlement is reached.

The reunited families have been eligible for government-funded mental health services, and the A.C.L.U. is arguing that the families should be offered a path to permanent status in the United States to compensate for the damage inflicted by the separations.

Lee Gelernt, who is leading the court case for the civil rights organization, said in court last month that discussions with the government were “moving very rapidly,” suggesting that a settlement may be imminent.

When advocates for immigrants discovered that children with U.S. citizenship had been separated from their parents, the advocates requested that those children, too, be included in the class-action lawsuit, to ensure that they would be eligible for the same remedies and services from the government as the broader group.

“This is about the unfinished business of redressing the cruel policy that devastated families and traumatized children,” said Mark Rosenbaum, a lawyer with Public Counsel, a public-interest law office that represented separated families in a related lawsuit.

“There is a whole group of families with citizen children that fell through the cracks,” said Mr. Rosenbaum. “These parents and children experienced identical harm.”

Separate settlement negotiations had for a time also included discussions of monetary compensation for migrant families. But reports in 2021 that the Biden administration was considering payments of up to $450,000 for each person affected by the policy drew criticism from conservative lawmakers, who said that people who had entered the country unlawfully should not be entitled to a large settlement. President Biden denied that such a sum was under consideration, and the government suspended the negotiations over damages.

Still, anyone wronged by the United States can bring claims against the government, and many families are doing so with the help of the A.C.L.U. as well as other groups and private lawyers.

Vilma Carrillo, who was separated at the Arizona border from her American daughter, Yeisvi, then 11, recalled watching as immigration officials near the detention center in Georgia where she was housed called one mother after another to reunite them with their children. She was never paged.

Instead, Ms. Carrillo said, she was returned to custody and later told that her child had been placed in foster care — because the child was American.

Foreign-born children were being returned more readily to their parents, immigration lawyers said, because they were being held in government shelters and could quickly be transported to their parents’ locations without going through the state bureaucracies of foster care systems.

Ms. Carrillo, who was detained by immigration authorities while Yeisvi was in foster care, was reunited with her daughter more than six months later, after a legal aid organization sued on her behalf. They are now living together in the United States.

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