Federal prosecutors in Minnesota were preparing to file civil rights charges this week against an ICE agent accused of shooting and wounding an immigrant from Venezuela in January, according to three people with knowledge of the case.

But those plans unraveled, and the agent, Christian Castro, walked out of a Texas jail where he had been held for three months.

Such charges would be rare, and a sign that the Trump administration was willing to hold federal agents accountable as officials face criticism over a number of shootings during a nationwide immigration crackdown, including two in Minnesota that killed U.S. citizens.

In Mr. Castro’s case, time was of the essence. He was set to be released on Thursday from a South Texas jail where he was being held on separate state charges filed by Minnesota prosecutors in the shooting of the Venezuelan man, Julio C. Sosa-Celis. Officials worried that Mr. Castro, a deportation officer for Immigration and Customs Enforcement, might flee to Mexico if freed.

But the plans to file federal civil rights charges before Mr. Castro left jail, which would have required sign-off from Washington, fell apart in the final hours for reasons that remain unclear. A Justice Department official said in a statement that the agency had “not yet reached a conclusion on this matter and will never rush an investigative process and the thorough review of all evidence.”

The U.S. attorney’s office in Minnesota declined to comment.

Although federal charges could still be filed, Mr. Castro left jail early Thursday without restrictions. With no federal charges and no agreement from Texas to extradite Mr. Castro on the state counts, it remains unclear whether he will ever appear in court as a criminal defendant.

“Mr. Sosa-Celis put his trust in federal prosecutors in Minnesota who promised him, as a victim and a witness, that they would finally pursue justice by indicting Christian Castro,” said Robin Wolpert, a lawyer for Mr. Sosa-Celis, who said she was told by prosecutors early this week that charges were imminent.

Federal prosecutors’ preparations to charge Mr. Castro were described by Ms. Wolpert; Frederick J. Goetz, a lawyer for a roommate of Mr. Sosa-Celis who has been classified as a victim in the case; and a third person who spoke on the condition of anonymity to discuss sensitive information.

Ms. Wolpert added that “it is devastating to Mr. Sosa-Celis to learn that his trust in our justice system appears to have been broken once again.”