The number includes some parents whom the government can't locate and those who authorities aren't certain are the parents of separated children. Hundreds more had been cleared and were just waiting on transportation.
On Tuesday, Homeland Security Secretary Kirstjen Nielsen told Fox News' "Special Report" that the Trump administration was "on track" to meet the reunification deadline. Nielsen declined to comment to reporters as she left the closed-door meeting.
The government said 64 parents didn't qualify to be reunited with their children because they had significant criminal histories or were otherwise "deemed ineligible".
Women and children walk to a bus in McAllen, Texas. Parents are typically equipped with ankle-monitoring bracelets and given court dates before an immigration judge.
Sara got out and was quickly in her mother's arms, asking her, "They're not going to take you away again, right?"
The futures of their children remain uncertain.
The deadline marks the closing of one chapter of the case, in which US District Court Judge Dana Sabraw ruled the government's practice of separating families for weeks and months at a time was inhumane and unconstitutional.
"These are troubling cases", ACLU said in the filing, requesting that the government explain its efforts to the court on how it plans make contact with these parents.
"In response to Thursday's court-imposed deadline for the government to reunite the almost 3,000 children over five it had separated under the "zero-tolerance" policy", Efrén C. Olivares, racial and economic justice program director for the Texas Civil Rights Project, said the U.S.is "failing in a crisis it created".
The Trump administration insisted it would meet the court deadline by reuniting all of the family members that it deemed eligible for reunification.
That number included 120 children whose parents declined to be reunited, 21 children whose parents had red flags in their background checks, 46 children who had a parent with a red flag for another reason, 79 children whose parents were released from government custody into the U.S. and could not be reunited, 431 children with parents who are no longer in the United States, likely those who were deported.
Romela Victoria Isaula and her 13-year-old son Geronimo were finally reunited after crossing the border near El Paso in May and being separated for two months.
"They're completely cut off from the outside world", she said. "My baby already had his hearing with a judge who signed his deportation eight days ago".
"Because they were fleeing violence and persecution in the first place, they in all likelihood can not return to where they were living before", Turner said.
Further updates are expected at Thursday's hearing. Both sides were due in court Friday.
Now the federal judge in San Diego who ordered the reunifications must decide how to address the hundreds of still-separated children whose parents have been deported, as well as how much time, if any, reunified parents should be allowed to file asylum claims.
The government missed the first deadline. The administration so botched this operation that it can not comply in a timely manner with the court's order to reverse course and reunite the families. 'It's the court oversight ... that has gotten us as far as we have.
"We have seen a lot of people come together over this, we're seeing the best of what Americans can be", she said.
The government gives advocates sometimes as little as an hour's notice when they're releasing parents and children, Garcia said. "The government shouldn't be proud of the work they're doing in separation".
Late last month, Sabraw ordered a nationwide halt to family separations, which Trump effectively did on June 20 following an global outcry.
As the deadline neared, small groups of children were led in and out of Lutheran Social Services in Phoenix all day Thursday, sometimes holding hands with a worker from the center.
All of the fathers, Reive said, "had no idea that they had signed a document that relinquished any rights to be reunited with the children".