The five protesters were shot on Friday during a confrontation with Bolivian police and troops outside the city of Cochabamba, Nelson Cox, a representative of the Ombudsman's Office, told Efe news. At least 22 others were wounded in the clash.
He blamed security forces for a "disproportionate" response to a group of cocoa growers marching toward Cochabamba for a protest against the self-proclaimed interim governmentled by Senator Jeanine Anez.
In response, the Bolivian National Police said the victims were killed after shots were fired by members of the protest march.
The police said that officers were attacked with "lethal weapons and improvised firearms at Huayllani bridge".
The ongoing protests in Bolivia broke out after the October 20 elections in which Morales was re-elected for his fourth consecutive term amid allegations of fraud.
Morales resigned on November 10 and flew to Mexico the next day for political asylum.
Anez took over as the interim leader of Bolivia, warning Morales that he faced electoral fraud and corruption allegations and that justice awaits him if he returned home.
Reacting to Friday's violence, Morales pleaded with police and soldiers to "halt the massacre".
Also on Friday, in capital La Paz and the neighbouring city of El Alto, thousands of supporters of Morales' leftist MAS party took to the streets again.
There were reports of the supporters clashing with the police.
( With inputs from IANS )