The figures show that 1,995 minors were separated from 1,940 adults from April 19 through May 31. The separations were not broken down by age, and they included separations for illegal entry, immigration violations or possible criminal conduct by the adult.
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Under a "zero tolerance" policy announced by Attorney General Jeff Sessions, Homeland Security officials are now referring all cases of illegal entry for criminal prosecution. U.S. protocol prohibits detaining children with their parents because the children are not charged with a crime and the parents are.
Sessions announced the effort April 6, and Homeland Security began stepping up referrals in early May, effectively putting the policy into action.
Since then, stories of weeping children torn from the arms of their frightened parents have flooded the media and the policy has been widely criticized by church groups, politicians and children's advocates who say it is inhumane. A battle in Congress is brewing in part over the issue.
Some immigrant advocates have said women were being separated from their infants; Homeland Security and Justice Department denied it. They also said the children were being well cared for and disputed reports of disorder and mistreatment at the border.
On Thursday, Sessions cited the Bible in defending the policy, arguing the recent criticisms were not "fair or logical and some are contrary to law."
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"I would cite you to the Apostle Paul and his clear and wise command in Romans 13, to obey the laws of the government because God has ordained them for the purpose of order," he said.
The International Rescue Committee, a humanitarian aid group, said in response that "a policy of willing cruelty to those people, and using young sons and daughters as pawns, shatters America's strong foundation of humanitarian sensibility and family values."
The new figures are for people who tried to enter the U.S. between official border crossings. Asylum-seekers who go directly to official crossings are not separated from their families, except in specific circumstances, such as if officials can't confirm the relationship between the minors and adults, if the safety of the children is in question, or if the adult is being prosecuted.
There were an additional 38 minors separated at ports of entry in May through June 6. There were more than 55 in April and a high of 64 in March, according to the figures.