Hours after an immigration agent fatally shot Renee Good inside her S.U.V. on a Minneapolis street last month, a senior federal prosecutor in Minnesota sought a warrant to search the vehicle for evidence in what he expected would be a standard civil rights investigation into the agent’s use of force.

The prosecutor, Joseph H. Thompson, wrote in an email to colleagues that the Minnesota Bureau of Criminal Apprehension, a state agency that specializes in investigating police shootings, would team up with the F.B.I. to determine whether the shooting had been justified and lawful or had violated Ms. Good’s civil rights.

But later that week, as F.B.I. agents equipped with a signed warrant prepared to document blood spatter and bullet holes in Ms. Good’s S.U.V., they received orders to stop, according to several people with knowledge of the events who spoke on the condition of anonymity because they were not authorized to speak publicly.

The orders, they said, came from senior officials, including Kash Patel, the F.B.I. director, several of whom worried that pursuing a civil rights investigation — by using a warrant obtained on that basis — would contradict President Trump’s claim that Ms. Good “violently, willfully, and viciously ran over the ICE Officer” who fired at her as she drove her vehicle.