The reason is an investigation into sexual abuse, where Morales is alleged to have had a child with a 15-year-old girl.
The arrest warrant, which still needs to be approved by a judge, was issued after the 65-year-old refused to testify in the case.
Morales ruled the South American country for 13 years until 2019. He is alleged to have made the teenager pregnant in 2016, which means that he, according to Bolivian law, has committed rape. He has previously denied the allegations and claimed that it is a conspiracy to prevent him from running in next year's presidential election.
On Monday, police who were supposed to arrest Morales were forced to back down after his supporters acted violently.
