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The federal grand jury in Castro's case returned a six-count indictment against him on Wednesday, reports CBS.
According to US media, officials expect to make the indictment public once Castro is in custody.
The charges against him come after the governor of Texas refused to extradite Castro to Minnesota, where he faces separate charges of assault and false reporting of a crime related to the shooting.
He was arrested in Texas in May and jailed for three months.
Castro was one of thousands of federal immigration officers deployed to Minnesota during Operation Metro Surge, which sparked fierce protests and resulted in the deaths of two US citizens at the hands of agents during confrontations.
Alfredo Alejandro Aljorna and Julio Cesar Sosa-Celis, who was shot in the leg and survived, were originally charged with forcibly assaulting, resisting or impeding federal officers.
After surveillance video raised questions about this version of events, federal prosecutors investigated the officers.
In February, ICE said two immigration agents might have made "untruthful statements" about the shooting. They were placed on administrative leave.
The charges against the migrants were dismissed, with prosecutors citing "newly discovered evidence", CBS reported.
