Three others were also arrested on charges that they had violated federal law during the church protest this month, reviving a case that was rejected last week by a magistrate judge.
A Border Patrol agent and a Customs and Border Protection officer have been on leave since Saturday, according to a Department of Homeland Security official.
Federal officers and protesters faced off in Minneapolis on Saturday, shortly after agents shot and killed Alex Pretti, a Minneapolis man, that morning.
Kristi Noem’s aggressiveness has sometimes given President Trump heartburn. She got a rebuke after a second killing by federal immigration agents but soon seemed to be back in his good graces.
The fatal shooting in Minnesota over the weekend was the latest episode in which high-profile efforts by Kristi Noem, the homeland security secretary, on behalf of President Trump’s policies have drawn intense criticism.
An initial report from an internal agency watchdog says the Minneapolis man was shot by law enforcement after resisting arrest, but makes no mention of the allegations leveled by a Trump administration official.
Dozens of refugees with valid status have been sent from Minnesota to Texas to be revetted, prompting a lawsuit. Those released have had to pay their way back.
Current and former officials describe growing frustration and disillusionment with the Trump administration’s approach, even as they support the goal of immigration enforcement.
The administration was in a race to control the narrative around the killing of Alex Pretti, even as videos emerged that contradicted the government’s account.
The rush to blame Mr. Pretti and exonerate the immigration agents deviated entirely from the way law enforcement investigations were normally carried out.
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