Asylum seekers looking to enter the US from its southern border will again be sent to Mexico while their claims are assessed, with the Biden administration announcing the reinstatement of the controversial “Remain in Mexico” policy on Thursday.

The US and Mexican governments haver agreed to a resumption of the program, put in place by Donald Trump in 2019, following its previous suspension by Joe Biden after he became president. It will initially begin in San Diego and in the Texas cities of Laredo, Brownsville and El Paso next week.

Biden had called the arrangement inhumane after it was used by Trump’s administration to return more than 60,000 asylum seekers across the border to Mexico, where they were often preyed upon by criminal gangs. Many people were left waiting for months in limbo in Mexico as their fate was determined.

In October, Alejandro Mayorkas, the homeland security secretary, said that the program “had endemic flaws, imposed unjustifiable human costs, pulled resources and personnel away from other priority efforts, and did not address the root causes of irregular migration”.

However, Republican officials in Missouri and Texas sued Biden’s administration in federal court to prevent the scrapping of the return to Mexico policy, claiming that it would place an undue burden on them from incoming migrants.

The supreme court ultimately concurred with the states, placing an injunction on the federal government in August which forced it to resume the program. Since then, federal officials have been negotiating with their Mexican counterparts on how the scheme will resume.

Under the reinstated deal, single adult asylum seekers will be the primary focus of the removals, with those transferred offered Covid-19 vaccinations. Mexico will accept asylum seekers from Spanish-speaking countries, the Washington Post reported.

The US will aim to complete migrants’ claims within 180 days, amid fears they will be left to languish in Mexico. The US Department of Justice is assigning 22 immigration judges to work specifically on these cases.

Supporters of the system have claimed it will help reduce the flow of migrants into the US but advocates have argued that there is little evidence that this will happen and point to the often dire humanitarian situation the program has exacerbated on the border.

People expelled by the US often end up in sprawling tent camps or sub-standard housing in places such as Tijuana and Reynosa that often lack basic foods and amenities for asylum seekers.

According to Human Rights First, a US human rights group, there have been more than 1,500 cases of reported kidnappings and attacks against migrants subjected to the system, known as Migrant Protection Protocols (MPP), and thousands more under another Trump policy known as Title 42 that uses public health concerns to eject asylum seekers.

“President Biden and his administration must stop implementing Trump policies that endanger the lives and safety of people seeking refuge in the United States,” said Eleanor Acer, senior director for refugee protection at Human Rights First.

“Remain in Mexico and other policies that flout asylum laws and treaties are inhumane and unjust. Every day they are in place, they deliver people seeking protection to places where they are targets of brutal attacks and kidnappings perpetrated by deadly cartels and corrupt Mexican officers.”

The Biden administration has also been sharply criticized by refugee advocates for the growing number of immigrants being held at private facilities. Biden had promised to end the private, for-profit jails but has exempted the Immigration and Customs Enforcement (Ice) agency from this effort and the number of immigrants in detention has nearly doubled to 29,000 since he took office.

“Frankly, it’s infuriating,” Setareh Ghandehari, advocacy director for Detention Watch Network, told the Washington Post. “It’s incredibly disappointing. We really expected more.”