United States officials have unveiled plans to shelter as many as 20,000 unaccompanied children on military bases as the issue of immigrant families crossing the US border continues to bedevil the Trump administration.

According to a report by The New York Times, the 20,000 beds at four bases in Texas and Arkansas will shelter “unaccompanied alien children”, Pentagon spokesman Lt. Col. Michael Andrews said on Saturday (Friday local time), essentially turning them into migrant camps.

Multiple government departments charged with handling the country’s current immigration crisis are scrambling to comply with President Donald Trump’s executive order that immigrant families be kept together.

It is unclear whether military housing would also be used to shelter the parents of migrant children.

Mr Trump was forced to back away from his “zero tolerance” policy earlier this week after it was revealed 2300 children had been separated from their parents at the US-Mexico border between May and June, sparking international and bipartisan outcry.

More than 2000 children have been separated from their families since ‘zero tolerance’ on migrants was declared. Photo: US Customs and Border Protection

The executive order called for detaining families at the same location.

There are multiple reports of widespread confusion on the border with lawyers and organisations struggling to reunite parents with their children.

About 500 migrant children of the 2300 have been reunited with their parents, officials with Department of Homeland Security said Friday. It is unclear how many of the 500 children are still being detained with their families.

“It’s just a total labyrinth,” attorney Jodi Goodwin told The Washington Post.

The Texas Civil Rights Project, a legal aid organisation representing more than 300 parents, said it had only been able to track down two children.

Akemi Vargas, 8, cries as she talks about being separated from her father during an immigration family separation protest.

Detained children are in the custody of the Office of Refugee Resettlement, part of the Department of Health and Human Services, and are being housed in foster homes and some 100 facilities scattered across the United States.

“Trump’s order leaves us with more questions than answers,” tweeted Democrat Senator for Virginia Tim Kaine on Friday. “How to ensure kids are safely returned to parents? When? Where are they being held? In what conditions? What care are they getting?”

Trump's order leaves us with more questions than answers:

How to ensure kids are safely returned to parents?
When?
Where are they being held?
In what conditions?
What care are they getting?

We'll keep asking because, lord knows, we can't trust this administration on its face.

— Tim Kaine (@timkaine) June 21, 2018

According to the Times, Border Patrol agents temporarily stopped referring immigrant cases to the Department of Justice for prosecution this week, contradicting the Trump administration’s “zero tolerance” policy of charging every adult who illegally crosses the US border.

On Thursday, the Department of Justice was forced to issue a statement denying the prosecution of immigrants travelling with children had been suspended.

Thousands of children continue to be housed in shelters, some converted Walmart stores, with the images of young children behind bars sparking a political maelstrom.

The White House was plunged further into crisis on Friday when First Lady Melania Trump wore a jacket emblazoned with the words “I REALLY DON’T CARE, DO U?” while visiting 55 migrant children being held at a shelter in Texas.

Ebony Bowden contributed reporting from New York City.