Many children were sent to government-contracted shelters or foster care hundreds of miles away from where their parents were detained.
More than 2000 children were separated from their parents by US immigration authorities at the border this spring before US President Donald Trump reversed course on June 20 amid an worldwide outcry.
The administration said in a statement that 57 children were reunified as of Thursday morning.
In total, 46 children under age 5 are still separated from the adults they were taken from at the border and are not eligible for reunification under court order at this time, in some cases because the parent was found to be unsafe or not actually a parent, according to the government.
When he was asked about the missed deadline, President Donald Trump blamed the immigrants who entered the United States illegally.
Twelve adults were not reunited with their children because the adults had been deported and the USA government is in the process of contacting them, the statement said.
Amna Nawaz talked with Lee Gelernt of the ACLU's Immigrants' Rights Project on Tuesday when the government didn't meet its first court-imposed deadline on reunification.
One immigration advocate told Reuters she was still awaiting details on when officials would return two children younger than 5 to their parents. They will be set free in the U.S. pending the outcome of their immigration cases, which can take several years. They saw I was not joking and they saw I was being very serious, ' he said.
In a response to the government's filing, the American Civil Liberties Union, which had filed the lawsuit against the administration over separated migrant families, maintained that it does not believe the government fulfilled its obligation in time.
The lead-up to the Monday court appointment indicated the duress the Trump administration is now under in trying to swiftly reunite the families it has separated - and just how messy the situation has gotten.
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"Although many medical professionals have graciously offered pro bono services for the children, who plainly are in desperate need of counseling, these medical professionals should not have to assume the costs associated with the government's policy", Gelernt wrote.
A federal judge gave the government until July 10 to reunify the 102 migrant kids under the age of 5 with their families.The judge ordered all migrant kids to be reunified by July 26.
Now the family detention system is at capacity - as are a network of about 100 shelters for migrant minors who traveled into the US without parents or a guardian and who now wait anywhere from a few weeks to years to have their cases resolved in the immigration courts.
"These are firm deadlines, not aspirational goals".
Suarez said activists will be watching the court ruling and will hold them responsible.
Of those 75, Justice Department attorneys told the court the government already reunited four children and would guarantee 34 others would be back with their parents by the end of Tuesday.
Government officials touted the screening process for parents, including background checks and DNA tests.
The government has pushed back on the idea that screenings should be streamlined, although officials said they will comply with the judge's order. The father held up his wrist and told reporters that after they were separated, he threatened to use a razor on himself if he couldn't speak to his son. "The reason they don't is the reason they brought the child in the first place was to get the child to the United States". Now, those well-intentioned hurdles are being set aside for families who were separated at the border.
Last December, the Trump administration quietly reversed an Obama-era directive that prevented Immigration and Customs Enforcement officers from detaining pregnant women except in extreme cases, altering the policy to prevent holding only women in their third trimester. The judge refused to modify that.