Earlier on Friday, air traffic controllers said they started a hunger strike in Brasilia's military-run control centre to protest against poor work conditions and equipment safety.
The civil air controllers' union, in a statement, said: "We have reached our human limits. We have no confidence in our equipment and no confidence in our commanders."
When controllers began striking, authorities demanded the controllers get back to work or face penalties.
|"We have reached our human limits [and] we have no confidence in our equipment and no confidence in our commanders"|
Civil Air Controllers' Union statement
Eighteen controllers were ordered arrested for having walked off the job and holed up at their workplaces, Globo television reported.
Jorge Botelho, president of the Flight Protection Workers Union, told The Associated Press: "All takeoffs are suspended due to the strike by military air controllers.
"There are a few civil controllers, but they are very few, so in effect all flights are stopped."
The air force, which is in charge of air traffic control, said all activity in the Brasilia control centre was stopped. Brasilia is the main traffic control centre for all flights through central Brazil.
Civilian controllers work side by side with military controllers in Brazil, but military controllers are not allowed to have unions.
The incident follows months of persistent disruptions in Brazil's air traffic system.
Jose Ulisses Fontenelle, former president of the Flight Controllers Association of Brasilia, said the controllers viewed the transfer of senior workers as a reprisal for slowdowns that controllers have periodically staged since Brazil's worst air crash last September.
Two jets clipped wings over the Amazon and one of them plunged into the rain forest, killing all 154 people on board.
Military officials have said air traffic controllers may have been partly to blame. Traffic controllers have complained they are understaffed and forced to rely on faulty equipment.
Members of congress and industry analysts have suggested taking control of the air traffic system out of military hands.
Walder Pires, the defence minister, on Friday said such a move would require a new law. He said the government was considering longer-term reforms.