The not-for-profit organization that operates a brand new US government detention facility for migrant youths says the last teenagers detained there will leave by the end of the week – just a few weeks after the center was opened and the media were taken on tours.

Kevin Dinnin, the chief executive of contractor BCFS, said on Tuesday that the facility in Carrizo Springs, in rural Texas, close to the US-Mexico border is expected to be empty by Thursday.

It is less than two weeks since the Guardian was given a lengthy tour of the center, with the government keen to demonstrate its safe, clean facilities. This was in contrast to appalling conditions for babies, children and adults being detained in border patrol stations after crossing the US-Mexico border unlawfully, which shocked visiting experts so much they went public.

At the time of that visit, just under 200 teens between 13 and 17 were held at the new Carrizo Springs secure facility, most having arrived from Honduras, Guatemala and El Salvador. The children had either entered the US alone or been separated from the adults who accompanied them across the border, and they had all been transferred from other facilities.

The total number of children had been expected to grow to 1,300 over the coming weeks, all housed in what the government terms a “temporary emergency influx facility”, which was expected to be kept open into 2020.

But the closure was abruptly confirmed on Tuesday, as first reported by Vice.

The US Department of Health and Human Services opened the facility just a month ago.

In response to a request for comment, the office of communications for the Health Department’s Administration for Children and Families (ACF) agency said: “We have no update on Carrizo Springs at this time.”

Carrizo Springs opened at the site of a former oil field camp and was supposed to help HHS take in children who were otherwise detained by the US border patrol in sometimes squalid conditions.

But the facility opened just as border crossings have fallen, after crackdowns by the US and Mexico on migrants traveling through Mexico and applying for asylum in the US. HHS has also sped up its processing of legal cases, in order to release children from detention faster, so they can join sponsoring families in the US while their cases proceed through the immigration system.

News of the closure was welcomed on Tuesday by Amnesty International USA, which believes the border crisis has been “manufactured” by the Trump administration and that detention facilities should be shut down and only utilized as the last resort.

“The closure of the Carrizo Springs facility makes clear the crisis is of the government’s own making. These temporary emergency facilities arose because of the government’s deliberate policy to punish children, resulting in the prolonged and indefinite detention of thousands of children,” said Denise Bell, researcher for refugee and migrant rights with the organization.

She added: “Temporary emergency shelters are never a home for children, and Carrizo and other detention facilities like it only demonstrate that these disastrous policies only endanger children and are never, ever in the best interests of the child.”

She said children should be with their families and the government’s policies of taking children seeking safety into custody were “unnecessarily cruel and shameful”.

The organization’s executive director, Margaret Huang, is testifying today on Capitol Hill about Carrizo Springs and the child detention center at Homestead, Florida, and the now closed camp at Tornillo, near El Paso, which was also run by BCFS.

The Associated Press contributed reporting