Washington (CNN) The Trump administration said Friday that it had reunified approximately 500 families separated at the border but the status of thousands more separated families remained unclear.

In a statement Friday evening, an administration official said that as of Friday Customs and Border Protection "expects that all unaccompanied children in their custody who were separated from adults who were being prosecuted will have been reunited with their families."

But the role of CBP is largely one of a clearinghouse before transferring immigrants apprehended crossing the border illegally to other agencies for longer term processing -- meaning any children in their custody had likely been separated from their parents within the last 72 hours, the length of time dictated by law that CBP can hold an immigrant child not with their parents.

The lack of further details about the thousands of children who had already been transferred out of CBP custody from the administration shows the disjointed government handling of parents separated from children at the border.

On Friday night, HHS confirmed it is working on a plan, spearheaded by the agency's emergency response division, to help put back together families that have been separated by the administration's zero tolerance initiative.

"Secretary (Alex) Azar is bringing to bear all the relevant resources of the department in order to assist in the reunification or placement of unaccompanied alien children and teenagers with a parent or appropriate sponsor," said HHS spokeswoman Evelyn J. Stauffer in a statement. "The Secretary has tasked the Office of the Assistant Secretary for Preparedness and Response with applying their operational and logistical expertise in addressing this complex effort. The Office of Refugee Resettlement continues to oversee and manage the Unaccompanied Alien Children Program."

More details on how the families would be unified were not immediately available.

As the children and parents were shuttled to separate government agencies under the effort, little planning appears to have gone into how they would be brought back together when the parents were finished with jail sentences for their criminal charges.

Now, case workers, lawyers and parents are scrambling to try to find their children through the maze of government bureaucracy and red tape surrounding their cases.

The government agencies caring for the parents and children have consistently declined to make clear exactly how many children are in the government's care as a direct result of the "zero tolerance" initiative begun last month to prosecute all adults for crossing the border illegally, thus separating those who have children while they face criminal charges. On Thursday, Homeland Security Secretary Kirstjen Nielsen said there were roughly 2,000.

A letter from Customs and Border Protection sent to congressional offices and obtained by CNN, said the 500 families figure was more than 15% of the total number of families that have been separated. By that math, the total number of separations would be more than 3,000.

"The administration continues to work to reunify prosecuted parents with their children," Customs and Border Protection congressional affairs staffer Pete Ladowicz in an email to congressional offices. "US Customs and Border Protection has unified approximately 500 children (over 15%) with their parents who had been referred for prosecution for illegal entry. US Immigration and Customs Enforcement and Health and Human Services are developing a process to be centered at ICE's Port Isabel Detention Center to continue unification efforts."

The administration has thus far only provided two overlapping figures for how many children have been affected.

From April 19 through the end of May, 1,995 children were separated due to the administration's zero tolerance policy, and 2,342 were separated from May 5 to June 9, according to Department of Homeland Security data. The policy to refer parents for prosecution was made public May 7 and the policy continued until Wednesday, when the President signed an executive order reversing course to keep families together despite any prosecutions.

It's not clear from this statement whether the reunified children were in HHS custody, as Customs and Border Protection hands children off to HHS and parents off to Immigrations and Customs Enforcement after they're finished being prosecuted. It's possible these were families that were only separated for the duration of the prosecution, and the children were never sent to HHS.

DHS did not answer follow-up questions.

When the prosecution policy went into effect, HHS became the natural place for the children separated from their parents, as under existing laws the agency cares for undocumented minors who enter the country illegally by themselves.

But to hand the children over, they were essentially redefined as unaccompanied migrant children -- subjecting them to the same HHS procedures as children who entered alone.

That meant that their cases, tracking information and the agency that was caring for them was completely separate from the organization caring for their parents -- and no planning appears to have gone into how the families would be reunited.

In recent days, ICE has been standing up its new reunification center -- but the agency has not answered questions about what, exactly, it would be responsible for there. Fact sheets on the DHS website implied it would be a place that parents could be connected with their children prior to being deported from the US.

Though criminal charges for the misdemeanor offense of crossing the border illegally take only a few days to resolve and the immigrants are usually only sentenced to time served, by the time parents emerged from Department of Justice custody, their children had already been sent to HHS shelters elsewhere in the country.

Parents and their representatives have been left struggling to find out where the children went, and because of secretive procedures protecting children in government custody due to privacy concerns, there is no straightforward way to look up a child in the system. Parents have been given hotline numbers to call that users describe as byzantine and hard to get through.

Also, once children are in HHS custody, procedures require that they be released to someone who qualifies as a "sponsor" under the agency's policies, which would almost certainly preclude an adult in DHS detention facilities, meaning parents can't be reunited until the government decides to release them or deport them.

Government agency procedures have mostly placed the onus on parents to track down their children. None of the agencies involved in the process have been designated as the central keeper of both parents' and children's data with the responsibility of putting them back together at the end.

The process to find one's child is "incredibly challenging, and what I fear is that it might, in some cases, be impossible," said Wendy Young, president of the advocacy and legal support organization Kids in Need of Defense and an immigration policy expert.