It is not clear how many people are involved. Mayor Jacob Frey says he will "continue to push" for the remainder of those involved in the operation to leave the city.
The federal immigration agency's operations in Minneapolis are being scaled back after the recent violence.
The announcement comes after the mayor spoke on the phone with US President Donald Trump.
"The president agreed that the current situation cannot continue," Frey said.
Trump previously announced via Truth Social that his border chief Tom Homan is on his way to Minnesota. He will meet with the mayor, among other people.
On Saturday, 37-year-old Alex Pretti was shot and killed by federal border agents in Minneapolis. Analysis shows Pretti approached the officers with a cellphone in his hand. There is no indication that he attempted to use the weapon he was carrying.
The incident has sparked protests in several US cities.
