Though federal authorities say they are acting as efficiently as possible to carry out the reunifications, some immigrant rights advocates say the policy is meant to deter potential asylum-seekers from Latin America

About half of 100 children under age 5 who were separated from their parents at the U.S.-Mexico border over the past two months have been reunited with their families, federal officials said Thursday.

Acting under a court order to reunite all 103 children by Tuesday, the Trump administration said 57 were with their families as of Thursday morning. Another 46 remained in government custody and could not be returned to their families because of safety concerns, deportations and other issues.

Government officials said they were acting as efficiently as possible to carry out the complicated reunifications after President Donald Trump altered his “zero tolerance” border enforcement policy that resulted in the removal of children to government-licensed shelters and foster care homes around the country while their parents were detained and criminally prosecuted for illegal entry.

But immigrant advocates on Long Island said the government had mishandled the reunifications and the delay was traumatizing the children. Some said the delays were intended to send a message to potential Latin American immigrants.

“It’s a punishment,” said Patrick Young, head of the Central American Refugee Center in Hempstead. “As much as the general public is horrified by the image of screaming children and hearing children begging for their moms, I actually think that that may be part of the purpose of this, which is for other potential asylum-seekers to hear that their children will be emotionally devastated if they try to come to the U.S. and apply for asylum.”

In a statement, the heads of the three federal agencies responsible for the process said: “Throughout the reunification process, our goal has been the well-being of the children and returning them to a safe environment. Of course, there remains a tremendous amount of hard work and similar obstacles facing our teams in reuniting the remaining families. The Trump administration does not approach this mission lightly.”

Javier H. Valdés, co-executive director of Brentwood-based Make the Road New York, said: “The Trump administration’s failure to meet the court’s deadline to reunite families separated at the border shows the administration’s ongoing neglect and disregard for the well-being of immigrants.

“The administration advanced a reckless, hateful policy that separated children from their parents, and has now failed to meet the court’s ruling that they must reunite them. We demand the immediate reunification of these families, an end to the so-called zero tolerance policy, and once and for all we must end family detention.”

MercyFirst, a Catholic agency in Syosset that works primarily with youth in foster care, is caring for 10 of the so-called border kids, though only one is under 5, said Gerard McCaffery, president and CEO of the group. However, the 4-year-old girl is not affected by the reunification because she came to the country under different circumstances, he said.

The government said it could not return 22 of the children because of safety concerns such as the parent having a criminal record or because authorities determined the child was not related to the person they were with at the border.

Another two dozen were not reunited because the parent had been deported or was in jail or prison for other offenses.

In some of the cases, the parent had serious criminal histories including child cruelty, murder or human smuggling. Seven were determined not to be a parent, one had a false birth certificate, and one had allegedly abused the child, government officials said.

“The seriousness of the crimes is the reason why we are not going to reunite them,” said Matthew Albence of Immigration and Customs Enforcement.

Young, who has worked as an immigration lawyer for more than three decades, said he doubted the government explanation, and had never seen such a high percentage of reunifications blocked for such reasons. “This is really extraordinary and unusual,” he said.

The 46 children will remain in the care of Health and Human Services, which will continue to seek to place them with a sponsor, such as other family members or in foster care.

It was unclear Thursday whether or how the 46 would be reunited with their families.

McCaffery of MercyFirst said the delayed reunifications were difficult for the children.

“The younger the child is who gets separated from their parent, the more traumatic it is for them,” he said. “The longer it goes on, the more likely that there could be some longer lasting damage to the youngster.”

“They took no steps from the time that the kids first came into care to really plan for their possible reunification,” he said, referring to the federal government. “So all of a sudden they are playing a lot of catch up.”

The administration faces a second, bigger deadline — July 26 — to reunite more than 2,000 older children with their families. Immigration attorneys say they already are seeing barriers to those reunifications from a backlog in the processing of fingerprinting of parents to families unable to afford the airfare to fly the child to them — which could cost as much as $1,000.