District Judge Dana Sabraw made the comments during a status hearing Tuesday in an ongoing lawsuit over the separations, two days before his deadline for the government to reunite those families.
"This is a remarkable achievement," Sabraw said, adding the government should be "commended."
During the hearing, the government said 1,012 families have already been reunited -- over 100 more than had been reunited by Monday evening's status update
Sabraw said he expects that his Thursday deadline will essentially be met and he expected to be satisfied by the next hearing Friday.
"For class members who are eligible, it appears that when we meet on this issue again on Friday that reunification will have been completed on time, which has to be highlighted and the government has to be commended for its efforts in that regard," Sabraw said.
But there are still 914 parents who are either ineligible or not determined, and Sabraw noted that that group likely cannot be reunited on time, even with the best effort by the government.
Going forward, he said the American Civil Liberties Union, which filed the lawsuit, needs "more information." He said the process needs to be even more "transparent."
"Some of this information is unpleasant," Sabraw said. "It's the reality of the case, it's the reality of a policy that was in place that resulted in large numbers of families being separated without forethought as to reunification and keeping track of people. And that's the fallout we're seeing. There may be 463, there may be more, it's not certain, but it appears there's a large number of parents who are unaccounted for or who may have been removed without their child."
He continued: "That's a deeply troubling reality of the case and the plaintiffs are entitled to that information. So there has to be an accounting."
Sabraw ordered the government to begin providing its lists of remaining parents to the ACLU on Wednesday, even if they are incomplete.
A little more than 200 parents have criminal records or declined to be reunified, more than 200 have been released, more than 460 are believed to not be in the country and another roughly 260 require further investigation, according to the government.
As for the 463 who are indicated as out of the country, the government could not say if they had all been deported without their children, as is likely. Justice Department attorney Sarah Fabian said the government was having to review each case file to figure out where that parent was.
"The records recorded reflect 463 with a code that suggests that they may have departed the United States. What I understand we are doing is taking a closer look at those," Fabian said. "So it may be a removal or it may be a voluntary departure that is unrelated to a separation or it may be a prior code."
'Things are a mess'
As the hearing turned to the ACLU's request to require seven days before reunified parents are deported to allow time to weigh the decision as a family, the organization raised the frantic conditions on the ground, some of which CNN has reported
"Talking to people on the ground now, and we have an enormous number of affidavits ... things are really a mess on the ground," ACLU attorney Lee Gelernt said. "I think you're going to be shocked when you see these affidavits."
Gelernt said that despite orders for communication between parents and children to occur, there was a "vast difference" between what had been ordered and what happened. Sometimes only one phone call between parent and child occurred. He referenced the form parents sign to authorize their deportation without their child, which is supposed to be given to them only if they have been ordered deported.
"Parents have no idea what's happening. They've signed these forms, many of them, to show you how much the confusion there is, many of them actually signed the forms giving away their child even though they didn't have a final order," Gelernt said. "There are group presentations ... the parents were put in groups of 50 and said, 'Here are your basic rights. You have three minutes to sign these forms.' "
The government grew openly frustrated with the suggestion that the ACLU would be filing the affidavits.
"I'm disappointed to hear that Mr. Gelernt is suddenly planning to file a raft ... of declarations. The government was caught off guard and quite by surprise when this motion was filed" in the first place, said Justice Department attorney Scott Stewart. "Now I get a signal that despite our significant jurisdictional objections, our days and nights trying to negotiate ... that we're about to be hit by a raft of affidavits."
He also disputed the accusations.
"We have many reasons to be very proud of this effort," he said. "So we strongly contest that characterization and look forward to the opportunity to present further views on that."
The judge asked for the ACLU to file its latest position by Wednesday.