WASHINGTON — President Trump’s executive order to halt family separations unleashed confusion in Washington and at the Mexico border Thursday, as Customs and Border Protection said it would it stop referring such cases for prosecution and migrant parents arrived at courthouses in Texas and Arizona wearing handcuffs, only to be led away without facing charges.

After a senior U.S. Customs and Border Protection official told The Washington Post that the agency would freeze criminal referrals for migrant parents who cross illegally with children, Justice Department officials insisted that their “zero tolerance” policy remained in force and that U.S. attorneys would continue to prosecute those entering the United States unlawfully.

On Capitol Hill, a hard-line immigration bill failed and a key vote on a more moderate version of the legislation was postponed. The Pentagon, meanwhile, agreed to house up to 20,000 unaccompanied migrant children on military bases in coming months. And despite the ongoing outcry over the separation of more than 2,300 migrant children from their parents since May 5, Trump administration officials gave no assurances the families would be swiftly reunited.

In scenes reminiscent of the botched “Muslim ban” in the early days of the Trump presidency, federal agencies Thursday were largely left to interpret the sudden changes hastily ordered by the White House a day before and figure out how to implement them. A family separation system that had been planned and tested over several months vanished at the president’s pen, with no stated plan to reverse its effects.

Administration officials held a meeting Thursday evening to grapple with the conflicting understandings of what the executive order was meant to do. People familiar with the discussions said the president had indicated his main goal was to lessen the public controversy surrounding separated families. Within the administration, however, the two main agencies following the order interpreted it very differently. The Justice Department filed court papers seeking permission from a judge to detain families together; Customs and Border Protection officials initially decided the order meant adults apprehended with children should be released, these people said.

The administration’s about-face leaves intact its “zero-tolerance” policy toward those who break the law, but the senior Customs and Border Protection official, asked to explain how the government would change enforcement practices, said Border Patrol agents were instructed to stop sending parents who arrive in the United States with children illegally to federal courthouses for prosecution.

“We’re suspending prosecutions of adults who are members of family units until (Immigration and Customs Enforcement) can accelerate resource capability to allow us to maintain custody,” the official said, speaking on the condition of anonymity to explain how the agency has interpreted and implemented Trump’s order.

A Justice Department representative said prosecutions would continue, but the decision to refer migrants for criminal charges after crossing illegally rests with the U.S. Border Patrol.

SESSIONS: ‘IT HASN’T BEEN GOOD’

Attorney General Jeff Sessions, who has embodied the administration’s hard-line stance on illegal immigration and was the principal advocate for its zero-tolerance policy, said in an interview with the Christian Broadcasting Network that the objective was not to take children away from their parents. “It hasn’t been good, and the American people don’t like the idea that we are separating families,” the attorney general told CBN Thursday. “We never really intended to do that.”

When Sessions announced the zero-tolerance policy in May, he warned that families who cross illegally would be split up. The move was condemned by multiple faith groups, including members of Sessions’s denomination, the United Methodist Church.

Maureen Franco, federal public defender for the Western District of Texas, informed defense lawyers Thursday that federal prosecutors in the jurisdiction were no longer bringing illegal entry charges against parents who cross the border with children, the El Paso Times reported.

A Justice Department spokesman declined to comment, but officials said repeatedly Thursday that the”zero tolerance” policy toward illegal immigration had not changed.

At two federal courthouses in Texas, large groups of migrants arrived to face charges Thursday – as the thousands of others have in recent weeks – but they were abruptly removed from court without being prosecuted.

In McAllen, Texas, 17 migrants who arrived to face criminal proceedings were told by their public defender that the charges were dropped, according to Efren Olivares, an attorney with the Texas Civil Rights Commission, who was in the courtroom. Olivares said he and others were interviewing the parents in an effort to reunite them with their children, adding that the parents had been weeping and begging for help before the announcement. It was unclear what would happen to the parents next, or when they would be reunited with their children, Olivares said.

Justice Department officials denied that any charges were dismissed, but they did not say why the migrants were taken to the courthouse but not prosecuted.

“The U.S. Attorney’s Office for the Southern District of Texas (SDTX) did not dismiss any immigration violation cases in McAllen federal court today,” the U.S. attorney’s office there said in a statement. “Media reports alleging SDTX cases were dropped or dismissed are inaccurate and misleading.”

A similar scene played out Thursday in a federal courtroom in El Paso.

In western Arizona, Border Patrol agents stopped separating parents from their children as of Thursday morning, according to acting chief patrol agent Carl Landrum, who added that parents crossing the border illegally with their children would no longer be referred for prosecution for illegal entry, although they would still face consequences because they would be transferred to ICE for deportation.

“What we are trying to avoid is saying that you were not going to be prosecuted,” he said. “That message would be very bad and that would translate to an increased number of people coming to the border and trying to enter illegally.”

“Did they break the law doing that? Yes, they did,” he said of parents crossing the border illegally. “Are they going to be held accountable? Yes, they will. Are we going to do that in a way that is as compassionate as possible? Yes.”

Landrum said he expected Trump’s executive order to compel more people to cross but that the effect probably would be delayed by several weeks. He did not know where families detained as a unit as a result of the executive order would be sent, deferring questions to ICE.

Homeland Security officials acknowledge that their ability to detain families is extremely limited – by law and by a lack of bed space. The agency’s three “family residential centers” have a combined capacity for about 3,000 adults and children, but they’re nearly full. So are ICE’s adult detention centers. That leaves the agency in the same bind faced by the Obama administration, at least until it can open new facilities that would meet family detention standards.

SPACE FOR DETAINEES RUNS OUT

With nowhere to hold thousands of additional families facing deportation, the Trump administration probably will be forced in the coming weeks to resort to the same “catch and release” practices it has vowed to end. Migrants will be let out of ICE custody while they await their court dates, sometimes with an ankle bracelet or some other form of electronic monitoring.

Because ICE lacks the detention capacity to rapidly increase the number of families it holds in detention, the senior Customs and Border Protection official acknowledged that many migrant parents and children probably will be let out of custody while they await court hearings.

Separately, the Justice Department filed papers Thursday in federal district court in a long-running legal case in California. Known as the Flores settlement, the ruling, which dates to 1997, curbs the government’s ability to detain migrant children and sets standards for their care. The Trump administration is asking for the court’s permission to hold families “together at ICE family residential centers pending the completion of [individual] removal proceedings.”

Top CBP officials said they had not known what the executive order would ask them to do until its release Wednesday. The decision to cease referring parents for prosecutionwas made by CBP and other Homeland Security officials for logistical reasons, the senior official said, because it would not be “feasible” for the agency to bring children with their parents into federal courtrooms.

Adults who cross into the United States illegally without children will continue to face misdemeanor charges, the official said. Most adults who enter illegally through the busiest span of the border – the Rio Grande Valley in South Texas – are sentenced to time served. But the official said the criminal prosecution of adults would ensure that lawbreakers face consequences.

“When a consequence is applied, it makes a difference on recidivism and illegal activity at the border,” the official said.

CBP officials will monitor migration patterns at the border to see whether the policy change leads to an increase in illegal crossings by family groups, the official said. “We’re going to watch closely and do what we need to do.”

Officials at the Defense Department also were drawn into the fray. A Pentagon official said the military has agreed to house up to 20,000 unaccompanied migrant children on bases after a formal request from the Department of Health and Human Services.

The Pentagon told lawmakers that HHS asked whether beds could be provided “as early as July,” and that the agreement would last at least through December.

The plan appears similar to one approved in 2014, when the Obama administration housed about 7,000 unaccompanied children on three military bases. The sites will be run by HHS employees or contractors working with them. They will provide care to the children, including supervision, meals, clothing and medical services.

HHS has about 12,000 migrant children in its care, nearly 10,000 of whom arrived without their parents. It was not immediately clear why HHS had projected a need for 20,000 temporary beds, given that Trump’s executive order will reduce the number of children taken into government custody.

HHS officials had no immediate comment.

“We have housed refugees,” Defense Secretary Jim Mattis said. “We have housed people thrown out of their homes by earthquakes and hurricanes. We do whatever is in the best interest of the country.”

Mattis, pressed on the sensitivities of the Trump administration separating children from their parents, said that reporters were going to have to ask “the people responsible for it.”

“I’m not going to chime in from the outside,” Mattis said. “There’s people responsible for it. Secretary Nielsen, obviously, maintains close collaboration with us.”

Mattis has approved temporarily detailing military attorneys to the Justice Department to help with the glut of immigration cases that have emerged on the border. The order, issued this month, calls for 21 attorneys with criminal-trial experience to assist as special assistant U.S. attorneys for 179 days, said Lt. Col. Jamie Davis, a Pentagon spokesman. They will assist in prosecuting border immigration cases, he added, “with a focus on misdemeanor improper entry and felony illegal reentry cases.”

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