Hundreds of supporters accompanied the nation's first Indigenous president as he crossed a border bridge to the town of Villazon on Monday, seen off by Argentine President Alberto Fernandez, who came to farewell him.

"I didn't expect to return so soon," Morales told the cheering crowd that met him.

Morales still faces charges of treason and sedition lodged by prosecutors under the conservative interim government that accused him of stirring violent protests and spent much of the past 12 months attempting to reverse his policies.

But a judge has cancelled the arrest warrant and the man who led Bolvia for almost 14 years apparently feels confident he is safe back home after a protege, former Economy Minister Luis Arce, was sworn in as president on Sunday after winning election with 55 per cent of the national vote.

Morales' Movement Toward Socialism party also retained its majority in congress.

Indigenous supporters of Morales greeted him at the border with chants of, "Evo! Evo!" as he launched a planned three-day caravan to the Chapare region where he rose to prominence as a leader of coca growers.

Arce has downplayed suggestions his mentor will play a major role in his administration, saying he won't govern "in the shadow of Morales" but the 61-year-old former leader remains the nation's most prominent figure.

He has not spoken about his plans, though many believe he will try to use his sway.

"Morales will try to influence because Arce was his minister and he was the one who chose him as candidate," said political analyst Carlos Cordero.

"With an opposition that has no great weight, Morales could be a rival or a good collaborator for Arce,"

Once overwhelmingly popular, Morales saw his support erode over his refusal to accept limits on his ability to seek re-election and over allegations of increasing authoritarianism.

Protests over alleged fraud roiled the nation when he claimed narrow victory in the 2019 presidential election, and he wound up resigning at the suggestion of military and police leaders.

He flew first to Mexico, and later moved to Argentina and was not permitted to take part in last month's election.

Human Rights Watch has said the terrorism charges against Morales appear to be politically motivated, though it also accused Morales' administration of similar judicial abuses.

Meanwhile, newly inaugurated President Arce has sworn in 16 cabinet ministers who will help him confront the COVID-19 pandemic and sharp economic contraction.

Australian Associated Press