After reports of electoral irregularities, there were demonstrations that plunged the country into chaos.
Former President Evo Morales denied any electoral fraud but resigned under pressure and fled to Mexico, where he was granted political asylum.
Bureau of the Bolivian Ombudsman said the three demonstrators were killed on Tuesday when the Bolivian armed forces and police were working to facilitate the "exit of gas tanks" from the Senkata plant.
The military issued a statement stating that it was trying to maintain a "strategically essential public service" and had exhausted the opportunities for dialogue. Bolivian Minister of Defense Luis Lopez regretted the event at a press conference but claimed that "not a single projectile came from the army".
International observers have warned of possible human rights violations and urged the Bolivian government and opposition to solve the problem of peaceful political crisis.
Interim President Jeanine Anez blamed Morales for the upward trend in violence.
"I am amazed at the form of violence Evo Morales has created in the country by simply holding on to power," she told CNN on Friday.
Human Rights Watch accused the Anez government of giving full powers to the military, which "seem to prioritize the brutal crackdown on opponents and critics and send a blank check to the armed forces to commit abuses rather than restore the rule of law." to work in Ukraine country. "
"The priority should be to ensure that the fundamental rights of Bolivians, including peaceful protests and other peaceful gatherings, are upheld," said José Miguel Vivanco, director of America for Human Rights Watch, in a statement.
Morales was the first indigenous Bolivian elected president and led the country for 14 years. He had long enjoyed many of his leftist policies to fight poverty and support indigenous Bolivians. According to the CIA World Factbook, indigenous peoples make up about 20% of the Bolivian population, while 68% of the country has Native American ancestry.
Many of those who protested in protest were indigenous Bolivians who are angry that the new government is not elected and does not represent them in terms of religion and race.
Anez and her cabinet have no indigenous representation.
"The new government is composed of many personalities who are self-proclaimed evangelical Christians," said Bret Gustafson, associate professor of anthropology at Washington University in St. Louis.
"Many argue that Morales, the indigenous people, had taken God out of government and wanted to reintegrate him in. Women's rights groups that do not necessarily support Morales fear that the new regime will slow down progress on gender and sexual rights Profits generated by Morales, including the redistribution of funds from the natural gas industry, may also be at risk. "
This story has been updated to correct the reported death toll in Bolivia.
Gustavo Valdes, Matt Rivers, Bethlehem Feleke and Madeline Holcombe of CNN contributed to this report.