"They come in with a child and they don't even know who the child is five hours before. And that's a shame," President Donald Trump said of immigrants arriving at the U.S. border.
A claim was made that three children suffered sexual abuse at the hands of shelter workers responsible for their care.
Judge Harry Leinenweber ruled the law the federal administration based its case on was unconstitutional.
The admission came amid a lawsuit in a Federal Court in Seattle.
The Trump administration has reportedly ordered at least 70 children under the age of 1 to appear before immigration judges since last October.