Gustavo Vargas, a retired air force general, has been arrested as part of an investigation into the crash.
The plane, operated by the tiny LaMia airline, was taking Chapecoense team to Colombia when it ran out of fuel.
Bolivian official Celia Castedo says she warned the pilot of the problem before departure.
She has now sought asylum in Brazil, saying she suffered threats and abuse.
Chapecoense were travelling to the city of Medellin to play the first leg of the Sudamericana Cup final against Atletico Nacional.
The British-made Avro RJ85 aircraft ran out of fuel as it approached the airport in Medellin on November 28.
In a leaked tape, pilot Miguel Quiroga can be heard warning of a “total electric failure” and “lack of fuel”.
Celia Castedo says she warned Miguel Quiroga before departure that the long flight between southern Bolivia and Medellin was at the limit of the plane’s maximum range.
She has now sought asylum in Brazil, saying she is being persecuted.
Her asylum process could take a year to be processed, the authorities in Brazil said.
Bolivian Government Minister Carlos Romero urged the Brazilian authorities to turn her back.
“What she has done is very serious,” Carlos Romero said.
“It’s a way of escaping the judicial system.”
Six people survived the crash. One of them, crew member Erwin Tumuri, said an initial stop for refueling in the northern Bolivian city of Cobija had been dropped by the pilot.
There was no warning to the crew or the passengers that the plane was facing electrical or fuel problems, Erwin Tumuri told Brazil’s Globo TV.
LaMia was originally registered in Venezuela, before moving its headquarters to Bolivia. It only had three planes, but only two of them were operational.
Chapecoense club, from the southern Brazilian city of Chapeco, was only founded in 1973 and had never reached a final of an international tournament.
A day after the tragedy, Atletico Nacional said it wanted to forfeit the title.
On December 5, the South American Football Confederation (CONMEBOL) declared Chapecoense officially champions of the Sudamericana Cup, the second most prestigious continental competition.
For its gesture, Atletico Nacional has been granted CONMEBOL’s special centenary fair play award.
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