The shooting happened after a car chase as tensions run high in the city since an agent killed Renee Good last week.
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In a statement, the Department of Homeland Security (DHS) said federal officers initially pursued the man in a car chase because he was illegally in the US from Venezuela.
The City of Minneapolis confirmed a man was shot and taken to hospital for non-life threatening injuries. An ICE officer was also taken to hospital to be treated for injuries, the DHS said.
Tensions over immigration enforcement have been running high in the city since the fatal shooting of 37-year-old Renee Nicole Good by an ICE agent on 7 January.
Good's death has sparked protests in Minneapolis, which have also spread to multiple other US cities.
The latest shooting prompted renewed clashes between demonstrators and law enforcement, the city's police chief Brian O'Hara said, adding his officers were hit by fireworks, ice and snowballs.
Minneapolis city officials said on X: "We understand there is anger. We ask the public to remain calm."
"The City of Minneapolis again demands that ICE leave the city and state immediately," they added.
In response to Wednesday's incident, a DHS statement said the man got out of his car and an altercation took place between him and an ICE official. It added that during the incident two other people emerged from a nearby apartment building and allegedly "attacked" the officer.
"Fearing for his life and safety as he was being ambushed by three individuals, the officer fired defensive shots," the DHS statement said, adding "both attackers are in custody".
The BBC could not immediately independently verify details in the statements. O'Hara said the FBI is investigating the incident.
In response to the latest ICE shooting, Minneapolis mayor Jacob Frey accused federal officers of "creating chaos" across the state.
Around 3,000 federal officers have been deployed to Minnesota over recent weeks.
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