The Trump administration says it has reunited more than 1,800 migrant children with family members by a court-ordered deadline.
This includes 1,442 children back with their parents in US immigration custody and 378 others released in “appropriate circumstances”, says a court filing.
But more than 700 children are not “eligible” to be reunited, including 431 with parents no longer in the US.
US officials separated more than 2,500 children from undocumented adults.
The US government instituted the policy in a “zero tolerance” crackdown on illegal immigration at the border with Mexico.
The 378 children released in “appropriate circumstances” include those reunited with parents who were already out of government custody, those sent to another relative or family friend, and those who are now over the age of 18.
Of the 711 deemed ineligible, 120 children’s parents had “waived reunification”, the government said on Thursday evening.
Dozens more remain separated because of “adult red flag”, referring to situations in which the child might be at risk.
San Diego federal judge Dana Sabraw ruled last month that all the detained minors separated under the policy should be brought back to their families by 26 July.
“By the court deadline this evening we are on track to reunite all eligible parents within ICE custody,” said Chris Meekins, of the Department of Health and Human Services.
But the American Civil Liberties Union (ACLU), which has sued the government over the policy, said US officials had only met “a self-defined deadline”.
ACLU lawyer Lee Gelernt told reporters: “The government shouldn’t be proud of the work they’re doing in separation. This is a disaster that they created.”
The organisation said it would try to trace the hundreds of parents no longer in the US.
But a former acting director of US Immigration Customs Enforcement, the US agency that rounds up undocumented migrants, said he fears many families will never be reunited.
“There is a very high likelihood that those parents are not going to see their children again,” John Sandweg told CBS News.
The Trump administration earlier this month reunited more than 100 migrant children under five years old with their parents, though it missed a court-ordered deadline to do so.
It said 57 of these youngsters were back with their families, though 46 others were deemed ineligible because of safety concerns, parental deportations, or other issues.
US President Donald Trump halted the family separations in late June after pictures of locked-up children and audio of them crying in distress triggered uproar.
But the reunions process has proved chaotic, with some children transported to see their parents only to end up back in their shelters after discovering their loved ones were not at the location.
The families were held after entering the US illegally, while others claimed asylum at border crossings, citing violence in their home countries of El Salvador, Guatemala and Honduras.
The children were being sent to various care facilities across the country while the adults were held in detention centres or prisons.