From 19 April to 31 May, a total of 1,995 minors were separated from 1,940 adults as they tried to enter the USA between official border crossings.
And the president signalled the drama could drag on.
A Department of Homeland Security official insisted that the minors were enjoying decent conditions. "If you smuggle illegal aliens across our border, then we will prosecute you".
"By and large, we are accepting almost all of the referrals that we get from our counterparts at DHS, we continue to work with the federal judiciary on practical solutions to differing caps that they have", said a Justice Department official. The House is expected to vote this week on a bill pushed by conservatives that may not have enough support to pass, and a compromise measure that the White House has endorsed.
Whereas angered protesters rallied at airports after Trump's first iteration of the Muslim-majority country travel ban, and internet users submitted public comments to the FCC supporting net neutrality, impeding the separation of families and holding the door open for vulnerable asylum-seeking immigrants feels far less actionable.
"I'm looking at both of them", he said.
Trump's opposition would deal a body blow to efforts to tamp down the border crisis, which has raised alarm among evangelical leaders who backed Trump's campaign.
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Yet several key Trump administration officials support the family separation policy, including Chief of Staff John Kelly, Homeland Security Secretary Kirstjen Nielsen and senior adviser Stephen Miller, a vocal supporter of stricter immigration laws.
Despite the family separation issue being a decision made by the Trump administration, officials have falsely sought to cast it as a Democrat-created dilemma. A 2008 anti-trafficking statute - signed into law by a Republican president, George W. Bush - also requires that certain unaccompanied alien minors be transferred out of immigration detention in 72 hours.
And on Sunday morning he retweeted a tweet from Saturday blaming Democrats for breaking up families.
Democrats went on the counterattack, with top House Democrat Nancy Pelosi calling the Republican proposal "simply unworthy of America".
On Thursday, Sessions cited the Bible in defending the policy, arguing the recent criticisms were not "fair or logical and some are contrary to law".
Trump stressed he opposes the separations.
"Look, I hope that we don't have to separate any more children from any more adults", Attorney General Jeff Sessions said last week. "Zero tolerance, it's a crime to come across illegally, and children get separated, ". As part of this renewed dedication to prosecute all cases of unauthorized immigration, children are being taken from their parents, processed, and detained in contracted "shelters" across the US, while parents are detained for prosecution instead of released.
The DHS official also rejected as "not true" various reports of wrongdoing, including the turning away of some asylum-seekers. The policy is leading to an increase in the number of detained immigrants being separated from their children.