Federal prosecutors charged an Immigration and Customs Enforcement officer who shot a Venezuelan man in Minneapolis with lying repeatedly about the circumstances of the incident in an indictment made public on Friday.

The officer, Christian Castro, faces six counts of making false statements in his account of the Jan. 14 shooting. He surrendered to federal authorities on Thursday and appeared before a federal magistrate judge in McAllen, Texas, where he lives, the next morning.

The federal indictment marked a rare instance of the Trump administration seeking to hold an immigration agent accountable for actions taken while on duty.

Mr. Castro entered a not guilty plea at Friday’s hearing. His lawyer, David A. Lindenmuth, said he expected Mr. Castro would be released later in the day on bond and that he would travel to Minnesota for future hearings.

Soon after the shooting, Mr. Castro told an F.B.I. agent that he fired his service weapon while lying on the ground after enduring a brutal, minutes-long assault by three men, according to the indictment. He told the agent that he had been repeatedly struck with a broom and a shovel before opening fire.

But surveillance video of the episode contradicted the officer’s account. Instead, prosecutors said in the indictment that Mr. Castro had been standing up when he shot a bullet through the front door of the residence and that he made demonstrably false claims about acting in self-defense.

On Friday, Mr. Lindenmuth, a former federal prosecutor, said there had been a rush to judgment in his client’s case.

“It feels like Mr. Castro is bearing the full force of the anger, distress and resentment of the people of Minnesota,” he said.

Mr. Lindenmuth said Mr. Castro had a long career in public service that included wartime service in the Army. His military service left him with a traumatic brain injury and a diagnosis of post-traumatic stress disorder, conditions Mr. Lindenmuth said led the Veterans Affairs administration to grant him a 100 percent disability rating.

Mr. Castro, 52, joined ICE last September, meaning he had only been an immigration enforcement agent for a few months at the time of the shooting. He has since been suspended without pay.

Mr. Castro also faces a separate set of criminal charges filed in state court in Minneapolis in May. In that case, he was charged with four counts of felony assault with a dangerous weapon and one count of making a false police report.

The state charges led to his arrest in Texas in late May and prompted a rare legal battle over extradition law after Gov. Greg Abbott declined to act on a request from Minnesota officials to extradite Mr. Castro. A federal judge sided with Texas, leading to Mr. Castro’s release from custody last week.

Mary Moriarty, the county prosecutor in Minneapolis who brought the state charges, said she was hopeful the federal charges would lead to Mr. Castro’s return to Minnesota.

“Despite Gov. Abbott’s best efforts to shield Mr. Castro, we will see him soon,” she said in a statement.

Mr. Castro’s account of the shooting was the basis of criminal charges of assaulting a federal agent that were filed against the man he shot, Julio Sosa-Celis, and his roommate. Both men are from Venezuela and did not have legal status at the time of the shooting. The government eventually dismissed that case after reviewing the surveillance video.

The indictment does not address the lawfulness of the shooting itself, which has been a source of debate within the Justice Department in recent weeks. And it did not reveal any new information about how the initial investigation was mishandled.

Career federal prosecutors in Minnesota sought to charge Mr. Castro with civil rights violations, which carry stiffer penalties. But they failed to get sign-off from top officials in Washington.

The disagreement over the charges led the Justice Department to fire one of the prosecutors who oversaw the case after an email the prosecutor wrote expressing his displeasure about the decision came to light earlier this week.

Justice Department officials in Washington said their investigation into the shooting remained open and that civil rights charges could be filed at a later date.

Gabriel V. Cárdenas contributed reporting from McAllen, Texas.