The F.B.I. is investigating whether drugs were inside a van last week when immigration agents killed the van’s driver during an encounter in Houston, according to a search warrant application signed by a federal judge on Tuesday.

A copy of the warrant application, filed in Houston federal court and obtained by The New York Times, described the search for “controlled substances” and included photographs of small bags inside the van, a white Ford Transit cargo van.

The van had been driven by Lorenzo Salgado Araujo, 52, who had been heading to a construction job in Houston on July 7 with three other passengers when agents with Immigration and Customs Enforcement began following them. After a pursuit, an agent shot Mr. Salgado Araujo in the abdomen, killing him.

“The United States is currently gathering all facts related to this incident, including what may have caused the occupants of the vehicle to flee,” Special Agent David McNeilly of the F.B.I. wrote in the search warrant application.

Neither Mr. Salgado Araujo nor the other men in the car were the intended target of the immigration enforcement action, according to a Department of Homeland Security spokeswoman. Instead, the agents had been searching for someone else.

Drugs were not the reason for the encounter, and there has been no indication that agents pursuing the van that day suspected drugs were present. There has also been no prior suggestion that Mr. Salgado Araujo or the others in the van had been involved with drugs or had any relevant criminal history.

Lawyers for Mr. Salgado Araujo’s family and for Victor Hugo Salgado Araujo, the victim’s younger brother who was in the van at the time of the shooting, declined to comment on the search of the van.

In the aftermath of the shooting, federal investigators have tightly controlled the evidence they have been gathering. Local officials, including the mayor of Houston and the Harris County district attorney, have said local investigators had not received the information they needed to conduct an independent investigation of the fatal shooting.

But the search warrant suggests that the investigation includes not only the circumstances of the killing but also possible criminal conduct by those inside the van.

The shooting has come under heavy scrutiny in Houston and nationally. Residents have called for the names of the ICE agents involved in the encounter to be made public. And since the shooting July 7, there have been numerous demands for an independent investigation.

Special Agent McNeilly wrote in the application that he “inspected the vehicle and observed in plain view several plastic bags with what appeared to be a white crystal-like substance packaged in small plastic bags.”

Specifically, the agent said, four bags were visible through the windows, and three bags were seen in the middle of the dashboard. Another bag was seen on the passenger-side floorboard.

The agent wrote that the packaging was “consistent with methamphetamine.”

The application was signed by Judge Richard W Bennett, a magistrate judge in the Southern District of Texas.

It was not immediately clear why the van had not been searched earlier, or whether the agents who obtained the search warrant found any drugs inside the van on the day of the shooting. A spokesman for the F.B.I. did not immediately respond to a request for comment.

The search warrant application also contained a brief narrative of the events that led to the shooting, according to the federal agent. The van had “refused to stop and instead drove over a median in an apparent attempt to flee,” the agent wrote, and was finally stopped “in the 6800 block of Canal Street,” on the east side of Houston. From conversations with other law enforcement officers, the agent wrote, he learned that the driver had been fatally shot by an ICE officer during the enforcement operation.

Seamus Hughes contributed reporting.