Bolivia's political crisis deepened as the country's military chief called on President Evo Morales to resign after his re-election victory set off of fraud allegations and deadly violence.

The appeal of Gen Williams Kaliman came after Mr Morales, under pressure pressure, agreed earlier in the day to hold a new presidential election.

"After analyzing the situation of internal conflict, we ask the president to resign, allowing peace to be restored and stability to be maintained for the good of our Bolivia," Mr Kaliman said on national television.

He also appealed to Bolivians to desist from violence.

Police dismantle a burning barricade during a protest against the re-election of President Evo Morales (Juan Karita / AP)

Mr Morales' claim to have won in the last 14 years in power.

The unrest has left three people dead and over 100 injured in clashes between its supporters and opponents.

Mr Morale agreed to a new election after a preliminary report by the Organization of American States found a "heap of observed irregularities" in the October 20 election and said a new vote should be held.

"We all have to pacify Bolivia," Mr Morales said in the statement to the nation's electoral court and urging the country's political parties to help bring peace.

Bolivians honked for horns and broke into cheers and applause in the streets as OAS findings came out.

Adding to the leadership crisis, however, the two government ministers in charge of mines and hydrocarbons, as well as the Chamber of Deputies and their other governments. Some said opposition supporters had seen their families.

Also on Sunday, the attorney general 's office says it will investigate the Supreme Electoral Tribunal for alleged fraud following the OAS report.

The man Mr Morales has been defeated, opposition leader and former President Carlos Mesa, said the OAS report showed "monstrous fraud," and he added that Mr Morales "can not be a candidate in new elections".

Mr Morales did not say that he will run again.