That's only about half of the 100 or so children covered by the court order.
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At a court hearing, Justice Department lawyer Sarah Fabian acknowledged the Trump administration won't meet the deadline for all the youngsters.
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She said the government was still working to do background checks and confirm the relationships between the adults and children in its custody.
More than 2,000 children in all were separated from their parents by U.S. immigration authorities at the border this spring before President Donald Trump reversed course on June 20 amid an international outcry and said families should remain together.
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Late last month, U.S. District Judge Dana Sabraw set deadlines of Tuesday to reunite children under 5 with their parents and July 26 for older children. On Monday, the Justice Department updated the judge on its progress.
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Before the court hearing, American Civil Liberties Union attorney Lee Gelernt said that a judge can impose sanctions, usually fines, for failure to meet a deadline but that the organization is not pressing for that at this time.
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He said the ACLU instead wanted a detailed explanation of when all families will be reunited.
"At this point what we need is very specific, concrete steps," he said.
Gelernt said the youngsters "have already suffered so much because of this policy, and every extra day apart just adds to that pain."
Click here for a look at immigration stories here in the Bay Area and around the country.