Transcript for Families hope to reunite with kids as debate over separation at the border continues
A mother scuies to greet her boy. But the reunion is stilted. The scar tissue of separation heart-wrenchingly painful. Difficult to break. Biana MARIA from guemala, her 7-year-old son taken from her a month ago. She's applied for political asylum. The U.S. Justice department agreed to release the boy after his mother sued the government. Legal action paid for by a pro-immigrant organization. Her message to other parents separated from their kids -- Reporter: The battle at the border is playing out in courtrooms across the country. Ever sin the trump administrati's zero tolerance policy went into effect. The way the law works, the first-time offenders that cross our border illegallyre guilty of a misdemeano those that cross multiple times are guilty of a felony. The president said, stop making the distinctions, marshal your resources, please arrest, catch, detain, and then prosecute everyone that crosses illegally. Reporter: Two days ago, president trump issued an executive order essentially stopping family separation. A senior white house official tellshe associated press around 500 children he been reunited since may, but there are mor than 1,800 still waiting. Civil rights lawyers say today marked a first. Today was the first day that we went in and money the people being criminally prosecuted for the misdemeanor of illegal entry, there were no parents. Reporter: However, the president's order did not spell ou just how to reunite those thousands of parents and children already in different detention facilities. Like the family of that little girl captured in audio first obtained by pro publica. 6-year-old Alison Valencia Madrid shown here with her mother, begging a supervisor to call H aunt after she and her mom were separated. Wednesday, pro publica was listening as the girl calleder aunt again from inside a detention center. Reporter: Her aunt didn't want her face shown, afraid speaking owl with affect her own asylum case. It's been a week since the girl and her mom crossed the border. Pro public reporting the girl is in a facility in Phoenix, over 1,200 miles from her mother, who is in por Isabel, Texas. Her aunt says mom was told they'd be reunited, but after filling out paperwork she hasn't heard anything else. For the first time since being separated, the mother and daughter talked on the phone on Thursday. The fact that she was able to memorize this phone number turned out to be a really lucky thing for her. Many of the kids who come to this country who are her age or below don't know things like phone numbers. They don't know their parents' full names. But that phone number distinished her from the rest of the group. Reporter: Those working closely on cases say big part of the problem, two totally different government agencies handle these cases. They should be able to put those children back with their parents just as fast as they took them away. There's no excuse for it. And they haven't provided one. Reporter: Adults captured at the border are prosecuted under the department of homeland security. Children go to E office of refugee resettlement, whi is under alth and human services. El Paso public defender Eric Henshaw says answering parents' questions about their children is difficult, and sometimes impossib. How's my child going to take care of itself? Where is my child? Why don't you know the answers to these questions about my child? I've never in my job had to say I'm sorry and say I have no good explanation for why someone would think this is the right thing to do in our country. Reporter: There's a phone line set up for parents to track their children. The idea here is to take the various children and the various facilities andreunite them with their parents through a pretty simple phone-based system. At that point we're going to have to develop a stable and sustainable system over time. Reporter: One thing the president's exetive order does make clear, families may now be kept together, but still in detention, perhaps indefinitely. There's inherent contradictio here. The president has said zero tolerance policy, you're going to prosecute everyone who cross the border illegally. You're also gointo try to keep famiies together. Does that mean jail them all? You have another court opinion that says you can't put children in certain kinds of detention facilities for longer than 20 days. Reporte indefinite detention of families is something critics and many democratic politicians say is unacceptable. Let's be clear about the executive order just signed the other day by president trump. It doesn't end. It doesn't end the zero tolerance policy. Doesn't stop cminalizing asylum-seekers. When you haveeople that show up that have no criminal history, and a child, and you purposely put them into a criminal court to felonize them, to turn them into a criminal on paper, and rip their child away, that's a totally different picture. Reporter: Several groups of lawmakers spent today touring some of those detention facilities. All the news media, I'm going to a you all to step off the property -- Reporter:alifornia democratic senator kamala Harris spoke at a rally outside a facility near San Diego. After visiting with migrant mothers inside who have been separated from their children -- These mothers have shared their stories, their personal stories, that are a story of a human rights abuse being committed by the United States government. Reporter: Today president trump chose to shift focus away from families separated at the border. These are the angel families. Reporter: Putting the spotlight on families whose loved ones were killed by undocumented criminals. None of our kids had a minute to say good-bye. We weren't lucky enough to be separated for five days or ten days. They're separate permanently. Reporter: Multiple studies show undocumented immigrants commit crimes at a lower rate than American citizens. Many of the parents being criminally prosecuted under zero tolence, their only crime was a misdemeanor of illegal entry. They're not vlent criminals. Reporter: Earlier this week, president trump went to capit hill repeating his message that congress needs T pass immigration reform, fund his wall, and solve family separations for good. The immigration system, it's been a really D, bad system, probably the worst anywhere in the world. We're going to try and see if we can fix it. Reporter: Yesterday house Republicans failed to pass a hardline immigration reform bill. Yeas 193, nays 231. Reporter: Today in an about-face president trump tweeted, Republicans should stop wasting their time on immigration until after we elect more senators and congressmen and women in November. While Washington struggles to find solutions, operations at the border keep churning. My colleague Marcus Moore was at this bus STO in southern Texas as a group of mothers arrived carrying their very young children. You can see they all have ankle monitors on. You may be able to see that. Reporter: The wen we spoke with say they weren't separated from their kids but they feared they would be. Instead officials processed them and tod released them. They are the fortunate ones. The relative few now fe to stay with family or friends. And wait for a ruling. The American dream is not yet the. And may never be. The aclu plans to file new pleadings for the migrants over the weekend and the government will submit a response on Wednesday.
This transcript has been automatically generated and may not be 100% accurate.