Public prosecutors in La Paz signed a warrant for police to detain the 60-year-old — who is in Argentina — and take him to the attorney-general’s office.
Morales fled Bolivia in November after civil unrest broke out following his re-election in an October 20 poll widely dismissed as rigged.
The former trade union leader denounced the arrest order as “illegal, unfair and unconstitutional” on Twitter.
“I’m not worried. As long as I’m alive I’ll continue with greater strength in the political and ideological struggle for a free and sovereign Bolivia,” he said.
Morales ruled the South American country for almost 14 years before resigning in November and leaving Bolivia.
He initially received asylum in Mexico and then arrived in Argentina last week.
The allegations against him stem from an audio recording released by Arturo Murillo, the interim government’s interior minister.
In the recording, Morales allegedly tells one of his supporters to block trucks and interrupt the food supply to several cities.
Morales was in Mexico at the time, the complaint alleges.
Murillo began legal action against Morales in November, after weeks of road blocks caused food and fuel shortages in the capital La Paz following his resignation.
The ex-President countered by accusing the interim government of manufacturing the audio to damage him politically.
The controversial October poll in which Morales was re-elected was annulled following an Organization of American States (OAS) audit that found clear evidence of vote rigging.
Right-wing deputy senate leader Jeanine Anez took over as interim president and has vowed to call new elections early next year, although no date has been set.
The interim government has barred Morales from standing in the ballot.
Bolivia’s constitution limits a president to two consecutive terms but Morales stood for a potential fourth term in October.
Ahead of the last two elections, the constitutional court — filled with Morales loyalists — made controversial decisions authorizing him to run again.
His detractors accused him of corruption and authoritarianism.
Speaking from Buenos Aires on Tuesday, Morales pledged to back another candidate from his Movement for Socialism party this time around.
“I’m convinced that we’ll win the next elections. I won’t be a candidate but I have a right to be in politics,” Morales told reporters.
“My obligation now that I’m not a candidate, now that I’m not president, is to accompany candidates so that they can win the elections,” added Morales, who was Bolivia’s first ever indigenous president.
Previously he insisted he’d been the victim of a coup and has launched near-daily Twitter attacks against Anez and her allies.
Earlier on Wednesday he claimed US President Donald Trump — who hit out against Morales on Tuesday for provoking violence in Bolivia from afar — was behind the “coup.”