The judge sided with migrants who have long complained about inhumane and unsanitary conditions in some US Border Patrol facilities.
The ruling came weeks after the conclusion of a seven-day trial in which attorneys for migrants who sued in 2015 argued that the agency holds immigrants in extremely cold, overcrowded, unsanitary and inhumane conditions.
The order makes permanent a preliminary injunction that US district court judge David C Bury issued in 2016 that requires the Tucson Sector to provide clean mats and thin blankets to migrants held for longer than 12 hours and to allow them to clean themselves.
Judge Bury is also banning the use of bathrooms for sleeping, which came to light during the trial this year, when video footage was shown of a man trying to reach a bathroom but failing to because migrants were sleeping in them.
Although the lawsuit predates last year's surge in immigrant arrivals, it illustrates some of the challenges posed when migrants are detained, especially if they are children.
Judge Bury has been critical of the agency, saying it has done little to remedy issues, especially around overcrowding and migrants' inability to sleep.
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