Morales has accused Bolivian security forces of "genocide" against his supporters in indigenous groups and appealed to the outside world to intervene.
Newly-appointed Interior Minister Arturo Murillo on Wednesday played a recorded phone call ahead of a press conference, in which a vote he attributes to Evo Morales urges an opposition leader in Bolivia to block and surround cities so that food does not reach the population.
"We are calling for the maximum penalty for rioting and terrorism," Murillo said on Friday, after a formal complaint was handed over to federal prosecutors.
The maximum sentence is 30 years in prison.
Evo Morales is in exile in Mexico and dismisses the allegations as a "father". The Socialist leader left the country after the results of the October 20 presidential election were questioned and protests flared up across Bolivia. Right-wing politician Jeanine Áñez has taken the place of interim president.