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.