Among the uncertainties that remain is what will become of the children who are still in federal detention, apart from their families because of various legal and logistical hurdles.

The parents of 30 of the children have been declared “ineligible” for reunification based on their criminal histories, though immigrant advocates have argued that some parents were unfairly included based on old or minor convictions that would not affect their ability to safely care for their own children.

The remaining 117 detained children all have parents who were deported without them, according to the report. A variety of volunteers and nongovernment organizations working with the federal government have been trolling through remote parts of Central America to try to find the parents — 11 of whom have not yet been located.

Of those who have been found, seven parents asked that their children be returned home. Those deportations were still pending as of Nov. 6, when the report was drafted. A total of 99 parents had waived their rights to reunification and left their children in the United States alone, presumably fearing what the child could face if sent home. For most families, that means violence, severe poverty, or both.

Evelyn Stauffer, a spokeswoman for Health and Human Services, said that the agency “takes its duty to care for all children referred to its care and custody with the utmost seriousness.” She added that the agency was still working to reunify the children with their parents or place them with sponsors, and that 92 percent had been discharged thus far. Those children who could not be placed with sponsors will remain in the agency’s care “until their day in immigration court, or until they turn 18,” Ms. Stauffer said.