The Bolivian government banned protests and meetings in Pando and said anyone carrying weapons would be arrested.
The government also said more bodies had been found following a clash on Thursday in which at least eight people were killed although it did not give a new death toll.
Opposition activists had allegedly shot dead farmers in Pando, an incident described by government officials as a massacre.
Protests had diminished elsewhere in Bolivia on Friday, although activists demanding greater autonomy continued to block roads across much of the east of the country.
Morales had said that despite pressure to show a "firm hand," he was the "first to ban the army and police from using firearms against the population."
|Protests have erupted in several
regions of Bolivia [Reuters]
"We're open to dialogue not only with the governors, but also with the participation of mayors and different social sectors," Morales said.
Protesters demanding greater regional autonomy and a bigger share of energy resources have taken to the streets in continuing protests across the country.
The protests have sparked a regional diplomatic row after Bolivia expelled the US ambassador, accusing him of inciting violent demonstrations, with the US responding by expelling the Bolivian envoy to Washington.
Hugo Chavez, the Venezuelan leader, then expelled the US ambassador to his country, in what he said was solidarity with the Morales government, with the US again responding by saying it would expel the Venezuelan envoy.
Dozens of Morales supporters gathered outside the US Embassy in La Paz, chanting anti-US slogans.
Lucia Newman, Al Jazeera's correspondent in Santa Cruz, said the decision to expel the US ambassador came amid Bolivian accusations of US interference into the country's affairs.
"The Bolivian government says that it has evidence that the US, and particularly the USAID aid agency, had been consorting with opposition leaders in Bolivia - and even funding them to bring about instability," she said.
"No concrete eveidence has been presented but these allegations have been around for a long time, The expulsion of the US ambassador at this time is the icing on the cake, and was something that many people here had been expecting."
An employee of the opposition-led regional government was also killed in the clashes and at least two people were killed and a dozen wounded in clashes in the northeastern town of Cobija, officials said.
The Bolivian government has blamed the unrest on the leaders of four states who demand greater autonomy and energy revenue and oppose his plans to change the constitution and distribute land to the poor.
South America's poorest nation has been in the grip of political turmoil for months.
Last month, Morales convincingly won a referendum on his rule but in the rebel states, voters also returned most of the governors forming the opposition coalition.
After failed negotiations to find a compromise solution, Morales announced a new referendum, to take place in December, to vote on his rewritten constitution, which would redistribute land and national revenues to give more to the indigenous population.