Luis Fernando Guarachi, the head of the Bolivian police’s Public Corruption Division confirmed to journalists in La Paz that the warrant had been issued.
Interior Minister Arturo Murillo tweeted a picture of what appeared to be the arrest warrant, adding: “FYI Senor (Morales).”
Morales left Bolivia for Mexico in mid-November after being granted asylum there, following intense pressure from the armed forces following a disputed election in what he has since described as a coup.
Morales moved to Argentina last week, just days after the inauguration of Peronist President Alberto Fernandez. Morales was granted asylum in Argentina and had requested “definitive refugee status,” Argentina’s Interior Ministry said.
The case against Morales in Bolivia centers on a video obtained by Murillo, a member of the interim government of President Jeanine Anez. She is a former senator and opponent of Morales who stepped into the presidency in November after Morales resigned.
Murillo last month filed a criminal complaint against the former socialist leader.
In the video, a Bolivian man is shown talking to someone on a speakerphone who appears to be directing plans for road blockades. Murillo said the voice on the speakerphone was that of Morales.
Reuters could not verify the authenticity of the video.
Morales, speaking to local television reporters in Argentina, denied that there was any proof of the accusation and called the warrant an act of intimidation.
“I have the right to defend myself. I want to tell you that I have already summoned some of our lawyers who are here,” Morales said.
Blocking roads is a common form of protest in Bolivia and much of South America. Blockades by Morales supporters have cut off fuel and food to some cities.