"It's a huge challenge operationally for our agents," McAleenan said.
Citing a background briefing from a CBP official, NPR's John Burnett reports that the agency's holding facilities are now overwhelmed: "Kids are waiting in cage-like holding cells, while their moms and dads go to court in shackles."
Detained in cavernous buildings and temporary camps, parents and their kids have languished through separations that in some cases have already lasted a month or more — exceeding the 20-day limit on holding children in federal custody. That limit is part of a decades-old settlement called the Flores agreement.
Several immigration experts say the government could speed up the process by adding more judges to the immigration system. But Trump disagreed, saying on Monday, "I don't want judges. I want ICE and Border Patrol agents."
Theresa Cardinal Brown of the Bipartisan Policy Center — who also worked on immigration policy under Presidents Obama and George W. Bush — tells NPR's Morning Edition that even before Trump took office, the U.S. was already struggling to deal with the number of immigration and asylum cases.
In April, the Justice Department said that nearly 700,000 cases were pending in immigration courts — a rise from 519,000 cases in 2016. The figure has steadily risen over at least the past decade.
"The backlog started in the Bush administration, but it really accelerated under Obama, because of the Central Americans arriving," Brown said. "Most Mexicans can be deported pretty immediately; Central Americans, again, often have due process — that created the backlog. The president saying he just wants to do away with the courts, you know, obviously [he] can't do that without Congress."
Brown says that while enforcement efforts developed a large security apparatus along the border, there was no correlating growth in the legal and justice system there.
"That's resulted in this backlog that takes two years," Brown said. "If we were to add more judges, reduce that backlog to a couple months — that would probably help with the problem the president is trying to address."
On Monday, Ashley Tabaddor, president of the National Association of Immigration Judges, told NPR that immigration courts' budgets have not increased along with those of law enforcement agencies:
"So we've seen a situation where, if you imagine a one-lane highway with one exit ramp being now built out to a three- or four-lane highway, and the exit ramp remains a single lane — and then trying to blame the exit ramp for the traffic."
For now, the border agency is one of many parts of the Trump administration that is calling on the Republican-controlled Congress to solve the problem, by passing a comprehensive immigration law.
When NPR asked CBP for clarification of its new approach to Trump's policy on Tuesday, the agency sent this statement from Andrew Meehan, assistant commissioner of public affairs:
"U.S. Customs and Border Protection is working through implementing the President's Executive Order in conjunction with the Department of Justice and is taking temporary action until Congress can find a lasting solution to family separation and we encourage them to act."