Acting Interior Minister Arturo Murillo said the complaint relates to a video in which Morales is supposedly heard in a phone call coordinating the blockades from Mexico, where he is living in exile since being ousted in a dispute over the Oct. 20 presidential election. Murillo said Bolivia's government is seeking a maximum penalty, which is between 15 and 20 years in prison.
Morales has said the video is a "montage" by his opponents.
Bolivia has been in upheaval since Morales proclaimed himself the winner despite widespread protests over allegations of electoral fraud.
Morales resigned on Nov. 10, after the military suggested he do so. He alleges he is victim of a coup d'état. Thirty-two people have been killed in protests and unrest.
The interim government also accused a former minister, Juan Ramón Quintana, of the same offences.
Juan Lanchipa, Bolivia's attorney general, confirmed that an investigation into the ex-president and the recording has been launched.
"This audio will be verified in Argentina, and we're also asking the telecom company to confirm where the call comes from," he said.
The blockades in Bolivia have hindered the free flow of goods throughout the country, in particular La Paz, where the government is located.
Late Friday, politicians both for and against Morales reached an agreement to send to congress a bill to convoke a new presidential election.
Sen. Oscar Ortiz from the interim government of Jeanine Áñez said the agreement would annul the Oct. 20 election. The bill will be introduced to the senate Saturday morning and if approved there, it will be sent to the chamber of deputies.
Earlier, members of Morales' party and the opposition had said they were near an agreement.
"We have advanced 95% on the agreement and we are really trying to progress as quickly as possible with all the political forces to call elections," Omar Aguilar, a senator with Morales' Movement Toward Socialism (MAS), told the Associated Press.
Opposition Sen. Shirley Franco said neither Morales nor his vice president, Álvaro García Linera, will be allowed to run. The exclusion is meant to honor the results of a 2016 referendum that rejected Morales' bid to change the constitution so he could seek a fourth term.
Efraín Chambi, who is a member of MAS, said that "the constitution should be followed."
At protests organized by Morales' supporters, people are no longer calling for his return. Instead, they are demanding Áñez resign over the killings and the use of the military to repress protests.