Thursday saw uncertainty among federal agencies on how to implement the measure, while parents did not know where their children were being held.
A senior Trump administration official told The Associated Press news agency that 500 of the more than 2,300 children separated from their families at the border had been reunited since May. It was not clear how many of these children were still in detention with their families.
The official, who spoke to AP on condition of anonymity, said federal agencies were working on a centralised reunification process for the remaining separated children and their families.
Trump signed the order on Wednesday after he came under political pressure for enforcing a policy that resulted in the separation of more than 2,000 children from their parents or legal guardians at the border.
His administration has taken a tough stance on what it deems to be unlawful crossings of the US-Mexico border and has vowed to prosecute the refugees and migrants who do so.
The separations have been a consequence of this prosecution, as minors cannot be held with their parents or legal guardians.
The “zero tolerance” policy will remain in place, despite the executive order.
Trump on Friday defended his tough immigration policy following criticism over the separation of families.
Speaking in Washington, DC alongside members of “angel families” – relatives of people affected by migrant crime – said he was highlighting an issue that has long been ignored.
Trump once again blasted media coverage saying, “you hear the other other side, you never hear this side”.
“More than 8,000 criminal aliens – these are really hardcore criminal aliens – were in police custody and were released because of our weak laws, weakest in the world, weakest in the history of the world. They were released back into our civilian population,” Trump said.
Al Jazeera’s Alan Fisher, reporting from Washington, DC, said Trump’s comments were an attempt to “seize back the narrative” by “playing to his base” that sees immigration as a significant issue.
Fisher added that Trump has so far reversed his position on a number of occasions, adding to the confusion.
“He said at one point, ‘only Congress can act; we can’t do anything’. And then by Wednesday, he was looking for an executive order when he really didn’t need an executive order; he could have just picked up the phone and changed his own Department of Justice’s policy,” Fisher said.
“He says he’s committed to ‘zero tolerance’, even though the executive order says that he won’t split up families, so no one’s quite sure how all that’s all going to work.”
Chaos ensued at the border as it was not immediately clear what the practical implementation of the order should be.
A Pentagon spokesperson said that space would be made available for 20,000 migrant children on four military bases, though it remained unclear if these beds would be for unaccompanied minors or families.
The Department of Justice (DOJ) asked a federal court on Thursday to alter the 1997 Flores settlement so that families can be detained together for the duration of their cases’ processing time. Under the settlement – which was expanded in 2016 to apply to accompanied as well as unaccompanied children – minors held with their families cannot remain in custody for more than 20 days.
The DOJ’s request prompted a continued outcry from rights groups, who say the Flores settlement is in place for a reason – to protect children from detention.
“Wednesday’s executive order, while purporting to stop future family separation, calls for families to be detained together, which was this administration’s goal from the get-go,” Lorella Praeli, of the American Civil Liberties Union (ACLU), said in a statement on Thursday.
With the executive order, Trump “paved the way to begin massive internment of families who come to the United States seeking asylum,” Praeli added.
“If the president thinks placing families in jail indefinitely is what people have been asking for, he is grossly mistaken.”
A lawyer with the ACLU told Reuters news agency that the organisation plans to seek an order in the federal court in San Diego compelling the reunification of immigrant parents with their children.
On Thursday, the federal public defender for the Western District of Texas told AP they would dismiss cases in which parents were charged with illegally entering or re-entering the country and were subsequently separated from their children.
Al Jazeera’s Fisher said that “it’s been a very difficult week” for the US president but noted that the a lack of clarity on the border, coupled with authorities’ confusion about how to reunite children who were separated from their parents and how to enforce the “zero tolerance” policy, next week “isn’t looking great either”.
In McAllen, Texas, prosecutors did not seek prosecution of 17 immigrants in light of the executive order.
The House of Representatives rejected a hardline immigration bill on Thursday and postponed a vote on a compromise bill to Friday.
Republican party members are divided on the compromise bill, which offers “Dreamers” a pathway to citizenship and frees up $25bn for construction of Trump’s border wall. Democrats oppose the law.
Protests against Trump’s border and immigration policies continued into the weekend.
In Portland, Oregon, dozens of protesters occupied the grounds of the local US Immigration and Customs Enforcement (ICE) office, forcing its closure on Wednesday. Similar protests are taking place in cities nationwide, including Los Angeles and New York City.
Mayors from about 20 US cities gathered at a holding facility for immigrant children in El Paso, Texas, on Thursday, accusing Trump of failing to address a humanitarian crisis he himself created.
“It is unclear whether the children being separated from their families are being treated as unaccompanied minors,” Seattle Mayor Jenny Durkan said.
“They do not know where these children’s parents are. This is a humanitarian crisis.”
The ACLU also questioned what happens to the children whose parents have already been deported or do not know their parents’ names or the countries they are from.
“The trauma that has been inflicted on these families is irreparable, and it is going to be a logistical nightmare to undo it,” the right organisation’s Praeli said.
“And the saddest part is that it didn’t need to happen.”