Gustavo Vargas, the chief executive of Bolivian charter airline LaMia, has been detained for questioning.
The company owns the plane that crashed over Colombia last week, killing 71 people.
Vargas and two other LaMia employees are being held at the prosecutor’s office in Santa Cruz before a decision is taken on whether to charge them with criminal failure to follow safety procedures or even manslaughter.
The plane is believed to have run out of fuel as it carried Brazilian football team Chapecoense, companions and journalists to the Copa Sudamericana finals in Medellin, Colombia.
A Bolivian air traffic controller says she warned pilot Miguel Quiroga the length of the flight was pushing the limits of the plane’s maximum flight time. Celia Castedo has since sought asylum in Brazil after reportedly being accused of negligence.