"Nobody likes" breaking up families and "seeing babies ripped from their mothers' arms," said Kellyanne Conway, a counsellor to the President.
Nearly 2000 children were separated from their families over a six-week period in April and May after Attorney-General Jeff Sessions announced a new "zero-tolerance" policy that refers all cases of illegal entry for criminal prosecution.
US protocol prohibits detaining children with their parents because the children are not charged with a crime and the parents are.
The Administration wants to send a message, said a Republican critic of the policy, "that if you cross the border with children, your children are going to be ripped away from you. That's traumatising to the children who are innocent victims, and it is contrary to our values in this country."
Maine Senator Susan Collins added that "we know from years of experience that we need to fix our immigration laws and that using children is not the answer."
Trump plans to meet House Republicans on Wednesday to discuss pending immigration legislation amid an election-season debate over an issue that helped vault the New York real estate mogul into the Oval Office in 2016.
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.
Conway rejected the idea that Trump was using the kids as leverage to force Democrats to negotiate on immigration and his long-promised border wall, even after Trump tweeted at the weekend: "Democrats can fix their forced family breakup at the Border by working with Republicans on new legislation, for a change!"
To Congressman Adam Schiff, (D), the Administration is "using the grief, the tears, the pain of these kids as mortar to build our wall. And it's an effort to extort a bill to their liking in the Congress."
Schiff said the practice was "deeply unethical" and that Republicans' refusal to criticise Trump represented a "sad degeneration" of the GOP, which he said had become "the party of lies."
-AP