Troops continued to arrive in Pando and were patrolling the streets of Cobija, the capital.
"There are people who want to continue sowing pain across the region," presidential spokesman Ivan Canelas told reporters on Sunday.
He said without providing details that highway blockades continued and that "an armed group" had set fire to the town hall in Filadelfia, a municipality near Cobija.
The La Paz newspaper La Razon quoted the country's highways chief as saying blockades had halted transit on major roadways in the opposition-governed eastern provinces of Tarija, Beni and Santa Cruz. The Associated Press could not immediately confirm the report.
The gravest challenge to Morales in his nearly 3-year-old tenure as Bolivia's first indigenous president stems from his struggle with the four eastern lowland provinces where Bolivia's natural gas riches are concentrated and where his government has essentially lost control.
The provinces are seeking greater autonomy from Morales' leftist government and are insisting he cancel a Dec. 7 referendum on a new constitution that would help him centralize power, run for a second consecutive term and transfer fallow terrain to landless peasants. Morales says the new charter is needed to empower Bolivia's indigenous majority.
The leaders of those provinces have designated the governor of gas-rich Tarija, Mario Cossio, as their representative and he was expected to arrive in La Paz on Sunday to resume talks on easing the crisis.
South America's leaders were also trying to prevent Bolivia from splintering apart. They were to gather in Chile on Monday for an emergency meeting called by President Michelle Bachelet. It was unclear whether Morales would attend, and President Alan Garcia of Peru was not expected.
Morales' representative in Pando, Nancy Texeira, said the death toll from Thursday's fighting between pro- and anti-Morales forces near the town of Porvenir was expected to rise as authorities continued to encounter more dead and wounded.
"We think there are more in the hills, people submerged in the river," she said.
On Saturday, Morales accused Pando Gov. Leopoldo Fernandez of using "Peruvian and Brazilian assassins" against Morales supporters.
Fernandez denied having anything to do with the violence, saying it was not an ambush but rather an armed clash between rival groups.
Presidency Minister Juan Ramon Quintana told local radio Red Erbol that authorities have arrested Fernandez "for violating the constitution and generating the bloody killings of the peasants."
A peasant leader involved in the street fight told the AP in a telephone interview Saturday that the violence began after he and several truckloads of companions came upon an opposition blockade on a jungle highway.
Antonio Moreno said there was some fighting - mostly with clubs and rocks - when a man emerged from a vehicle and fired on peasants with a submachine gun.
"The campesinos fled to the mountain, while others jumped into the river," he told the AP.
Morales and ally President Hugo Chavez of Venezuela expelled the U.S. ambassadors in their countries last week to protest what they called Washington's inciting of the anti-government protests.
The departing U.S. ambassador to Bolivia, Philip Goldberg, denied the accusations on Sunday in his first public comments on the matter.
"I would like to say that all the accusations made against me, against the Embassy and against my nation are completely false and unjustified," he told reporters in La Paz. "I have nothing to say to those who misinterpreted my actions."
Morales has offered no detailed evidence of Goldberg's alleged conspiracy with the opposition. He has, instead, accused Goldberg of egging on anti-Morales forces through meetings with governors who have publicly called for the president's ouster.
Meanwhile, Chavez insisted he would intervene militarily in Bolivia if Morales were toppled or killed.
In a speech Saturday in Venezuela, he accused Bolivia's military brass of not fully supporting their president, of "a work stoppage of sorts."
Bolivian armed forces chief Gen. Luis Trigo earlier in the week rejected Chavez's pledge to intervene, saying no foreign troops would be permitted to set foot on Bolivian soil.
On Sunday, Defense Minister Walker San Miguel backed his armed forces chief.
"We Bolivians will resolve our problems among ourselves," he said in an interview with the state TV network.
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