The referendums, triggered by constitutional amendments to redistribute wealth among the richest and poorest regions of the country, were held on Sunday, nearly a month after the prosperous province of Santa Cruz voted overwhelmingly for autonomy. Exit polls report that some 85% of the Pando and Beni provinces voted for autonomy from central government. The final results of the referendums are expected within five days.
A fourth province, Tarija, is to hold a referendum on June 22.
The country's interior minister Alfredo Rada slammed the referendums as "illegitimate, illegal, unconstitutional and separatist."
Critics of Sunday's polls pointed to the referendum's relatively low turnout, with around 50% of those eligible to vote casting their ballot. There were reports of clashes between pro and anti-government supporters during the voting.
Evo Morales, who became the country's first indigenous president in 2005, has pushed for amendments to the Bolivian constitution that would see a redistribution of land, as well as gas and oil revenues. On May 1 the government took control over the extracting, processing and transportation of oil and gas.
The landlocked nation has the second-largest reserves of natural gas in South America, but the indigenous people who make up two-thirds of the population largely exist in poverty as political and economic life is mostly dominated by descendents of Spanish colonists.
"It's not a problem of autonomy," Morales said on Sunday. "The problem is that they can't accept that an Indian from the countryside is their president."
A nationwide vote of confidence in the president and eight regional governors is due on August 10. Morales has over two years left in office.