The Trump administration has opened the door to a seismic overhaul of immigration and asylum procedure that could lead to the indefinite detention of thousands of asylum seekers who cross the border illegally.

The US attorney general, William Barr, on Tuesday issued guidance overruling a precedent set by George W Bush’s justice department in 2005, which enshrined asylum seekers’ right to bond, irrespective of how they entered the country.

Barr stated in his updated guidance that the 2005 decision was “wrongly decided” and he would move to block immigration judges from offering people who have crossed the border illegally and have established a reasonable claim of torture or persecution the chance of release as their cases are decided in immigration court.

With the immigration court backlog at an all-time high – there are close to 900,000 pending cases – asylum seekers are waiting over 1,000 days on average for their cases to be processed, meaning Barr’s decision could lead to the indefinite detention of thousands of people.

Immigration enforcement is currently holding a record number of people, more than 50,000, in detention as part of the Trump administration’s broad crackdown on migrants. Barr’s decision is likely to significantly add to that number as the Department of Homeland Security [DHS] prepares to erect new tent detention facilities close to the border.

A footnote included in Barr’s decision revealed that homeland security had requested that the attorney general delay his decision on bond “so that DHS may conduct necessary operational planning” to accommodate the change. The ruling will not go into effect for another 90 days.

Children seeking asylum are currently protected by a separate ruling from a federal court in California that ordered they must be released from detention after 20 days. The Trump administration, which has pledged to end the policy of so-called “catch and release”, has unsuccessfully tried to reverse this ruling.

A justice department official did not immediately respond to a request for comment on whether the department would seek to use Barr’s new rules in cases involving families and children.

Human rights groups met Barr’s decision with immediate condemnation.

“Seeking asylum is a human right, not a crime, and families forced to flee for their lives shouldn’t be treated like criminals” said Charanya Krishnaswami, Americas advocacy director for Amnesty International USA. She argued the decision could force parents to decide to either be locked up with their children indefinitely, or relinquish custody of them for the duration of a months- or years-long approval process. “This is both a heartless punishment against vulnerable people, and a potential back-door way for the administration to separate families. This decision must be reversed,” she added.

Mary Bauer, the deputy legal director of the Southern Poverty Law Center, argued that the decision would be “essentially depriving parents of the right to be with their children and condemning those who have already experienced extraordinary trauma to even greater suffering”.

The American Civil Liberties Union [ACLU] said it planned to sue the government over the decision.

“This is the Trump administration’s latest assault on people fleeing persecution and seeking refuge in the United States,” said Omar Jadwat, director of the ACLU’s Immigrants’ Rights Project. “Our constitution does not allow the government to lock up asylum seekers without basic due process. We’ll see the administration in court.”